User talk:Chanely/sandbox

Assignment 1 - Critique of Bacterial circadian rhythms

All experiments mentioned were appropriately cited using credible, objective articles from scientific journals. However, the page lacks several sources to support current knowledge and claims. For instance, the lead paragraph defines bacterial circadian rhythms and mentions “it was thought… eukaryotic cells had circadian rhythms” without citing the origin of this information. The claim “It is now known that cyanobacteria…have well-documented circadian rhythms…” does not refer to who knows this fact or any of these ‘well-documented’ systems. The author should include a reference for every new fact stated and specify its source (who claimed this?).

The author also includes many personal arguments against the historical belief that only eukaryotes had circadian systems. These non-objective opinions, along with biased adjectives like “the most spectacular…” and “ground-breaking study”, should be omitted. Important findings on eukaryotic circadian mechanisms, potential consequences of disrupted rhythms, and the relation between these systems and metabolism are significantly underrepresented and should be included. The article heavily focuses on cyanobacterial systems and should further elaborate on the current state of research beyond cyanobacteria, such as inconclusive studies or research limitations.

The headings “History: are prokaryotes capable of circadian rhythmicity?” and “Visualizing the clockwork’s gears: structural biology of clock proteins” are not concise. Instead, the headings could be reworded to “History of circadian rhythm research” and “Structure of clock proteins” so readers immediately understand their corresponding content. Mentioned jargon and vague language, such as “bona fide circadian rhythms”, “molecular clockwork”, and “global gene expression”, should link to pages on those topics.

Chanely (talk) 22:51, 15 September 2017 (UTC)

Assignment 2 - Choosing an Article: Purple bacteria

The article Purple bacteria has high notability as thorough research exists on the structure and function of purple bacteria, the chemistry involved in their metabolism, and their phylogeny. Thus, the article should be improved to more accurately reflect current knowledge of purple bacteria and metabolism.

To improve the article’s Metabolism section, vague explanations and wording should be clarified. For instance, the author describes that in purple sulfur bacteria (PSB), “it is either sulfide or elemental sulfur” without specifying what “it” refers to. Purple non-sulfur bacteria (PNSB) “use hydrogen” yet its role in metabolism is not explained. These sentences should clarify that electron donors for PSB and PNSB are sulfide or sulfur, and hydrogen, respectively. P870 is referred to as a “special pigment pair” without an explanation of the term or an external link to an article. P870 should be defined as a chlorophyll pigment located in the reaction centre which is excited by photons. As well, the paragraph does not explain how charge separation relates to quinone reduction and how quinones are oxidized. These steps can be coherently linked using details such as: excited electrons from the reaction centre reduce quinone Q_B. This forms hydroquinone Q_BH which is oxidized by the bc₁ complex, an exergonic reaction fueling proton pumping into the periplasm.

The article should omit irrelevant details, such as that PSB and NSB “were considered families, but RNA trees…”. This relates to phylogeny and should not belong under Metabolism.

Additionally, the article lacks important information that would better illustrate purple bacteria metabolism. It mentions the cell membrane “is folded…to form sacs, tubes, or sheets…increasing the available surface area” without explaining its significance or much detail. The sentence could be revised to be the cell membrane “is folded…to form vesicle sacs, tubules, or single-paired or stacked lamellae sheets. This is called the intracytoplasmic membrane which increases the available surface area to maximize light absorption. The article should also explain which “other compounds other than hydrogen” are PNSB electron donors, such as organic acids and sulfides (but not at high concentrations like PSBs).

--Chanely (talk) 00:44, 24 September 2017 (UTC)

Chanel Trac's Peer Review

The edit does a good job reorganizing what was initially written into a more in-depth and accurate explanation of the metabolic mechanism of purple bacteria by refining the information. Being an important defining feature of purple bacteria, the placement of the section was aptly introduced after the article’s main description. While minor, perhaps general purple bacteria metabolic mechanism could be introduced first, and then include a subsection to explain the metabolic features of the different purple bacteria types to improve the article flow.

The content reflects the important points of its metabolism, such as its photosynthetic related structures, cyclic electron transport, and the metabolic differences between the two purple bacteria types in an organized manner. There is no redundancy present, with each statement being necessary. While not missing anything very important, maybe a short general description on what type of molecule P870 transfers its electrons towards in the ETC, and not just “cytochrome” would help.

Appropriate sources for each statement was made use of to bolster the credibility of the information, with each reference being from independent scientific journals and academic textbooks such as PNAS. For instance, the edit appropriately uses findings in “Modeling the electron transport chain of purple non-sulfur bacteria” to validate purple bacteria’s cyclic electron transport. Furthermore, there was no overburdening one source with multiple statements.No presence of paraphrasing or bias was observed, and possessed neutral information delivery. The use of “thus”, however, could be misconstrued as drawing to unwanted conclusions.

The writing wasn’t too complex to confuse readers, while still providing concise information on purple bacteria. Also, the grammar, structure, and sentence flow were sound. If ever, the explanation of the ETC progression could be changed, as it could be perceived as electrons in P870 being moved directly to those other cytochromes.

Jgggana (talk) 02:05, 9 November 2017 (UTC)