User talk:Sddem/sandbox

Bacterial Circadian Rhythms

This article contained very broad and somewhat vague information regarding bacterial circadian rhythms. It included a large ‘History’ section that described reasons behind different circulating theories about the topic over the years, however beyond that, there is a little scientific elaboration. For instance, throughout the article, only bacterial circadian rhythms that were dependent on light/dark cycles, and temperature were mentioned. This leaves the information presented in the article out-dated, and through omission of current research, inaccurate; a paper published in 2016 found that bacterial circadian clocks are “set” by metabolic activity, not light and dark cycles as is mentioned. ^[1]

Furthermore, this article fails to expand on the more relevant scientific matters. The History subtopic contains three paragraphs of mostly superfluous material that contributes little to the audience’s scientific understanding, while important subjects, namely “Relationship to Cell Division”, are short and undeveloped. This lack of information is likely to leave readers assuming there is little known about this topic, which is inaccurate, as entire papers have been published describing their relationship and importance. ^[2]

Additionally, there are some superficial details that could help in improving the article. For instance, the author failed to hyperlink any of their references, which makes it inconvenient for a reader to follow-up on any of the sources. As well, the author’s choice in terms, such as “apparently”, and circuitous syntax in places makes the article seem weak and undeveloped to a scientific audience.

References:

[1]: Pattanayak, Gopal K. et al. “Controlling the Cyanobacterial Clock by Synthetically Rewiring Metabolism.“ Cell Reports, vol. 13, no 11, pp. 2362 – 2367, http://www.cell.com/cell-reports/pdf/S2211-1247(15)01346-7.pdf

[2]: Johnson, C. H. (2010). Circadian clocks and cell division: What’s the pacemaker? Cell Cycle, 9(19), 3864–3873. http://doi.org/10.4161/cc.9.19.13205

Sddem (talk) 05:21, 18 September 2017 (UTC)

Microbial Cooperation

The topic of cooperation between organisms has historically been dominated by evolutionary studies of eukaryotes, specifically between complex animals.^[1] However, in the past few decades, research has turned its attention to cooperation among microbes. The number of studies done regarding microbial cooperation have been published in internationally acclaimed journals, such as The Annual Review of Ecology, Evolution, and Systematics, and Proceedings of the Royal Society and increased nearly 10-fold over the past two decades. Microbial cooperation also contains popular subtopics that have their own range of significant coverage, such as quorum sensing.

While this article provides a lot of detail, its overall topic is broad and diverse. Therefore it is unnecessary and inefficient to provide detailed background information to every new concept introduced throughout the article. Instead, it would be advantageous to reduce the number of lengthy examples and general descriptions in both the subtopics, and expand more on its relationship to microbes and their communities, as they are currently lacking in support and proper explanations.

For instance, the article mentions siderophores within the Mutualism subtopic. However, its brief mention only leaves the impression that surrounding bacteria benefit from the host’s extracellular secretions by chance. This is not the case, as there is a documented positive correlation between the relatedness of a bacterium (the host) with the surrounding bacteria, and its production of siderophores. This suggests that the bacteria are intentionally affording fitness to organisms containing similar genes, a fact that is incredibly more significant than the initial impression. ^[2]

Additionally, the article would be greatly improved by replacing the example used in ‘Altruism’. The author includes a description of programmed cell death (PCD) to explain how some bacteria will undergo apoptosis to provide benefits to other bacteria in the community. However, this example is still in the process of being theorized, and lacks concrete evidence explaining the cause and mechanisms behind it.cite A suggested improvement would be to use an example that has been described and modeled in studies to a greater degree, such as the cross-feeding enzyme of Bacteroides ovatus, or bacterial protection mechanisms to antibiotics. ^{[3] [4]}

References

[1]: Joel L Sachs , Ulrich G Mueller , Thomas P Wilcox , and James J Bull , "The Evolution of Cooperation," The Quarterly Review of Biology 79, no. 2 (June 2004): 135-160.

[2]: Stuart A. West, and Angus Buckling, “Cooperation, Virulence and Siderophore Production in Bacterial Parasites,” The Royal Society 270, (July 2002): 37-44.

[3]: Rakoff-Nahoum, S., Foster, K. R., & Comstock, L. E. (2016). The evolution of cooperation within the gut microbiota. Nature, 533(7602), 255–259.

[4]: Lee, H. H., Molla, M. N., Cantor, C. R., & Collins, J. J. (2010). Bacterial charity work leads to population-wide resistance. Nature, 467(7311), 82–85.

Sddem (talk) 06:41, 28 September 2017 (UTC)

Selina's peer review

The structure of the edited and the original versions remained mostly the same. I appreciated the logical flow which started with an overview of mutualism as a behaviour, then narrowing it down to microbial communities, elaborating on a specific example of mutualism with siderophores, and finishing with why this behaviour is evolutionary favourable.

The little content that was added was relevant to the topic, explanation on the significance of siderophores were concise and sufficient for the article's purpose. The statement regarding mutualism benefiting the passage of genes as a community was well done. Perhaps the volume of the added content could be improved upon with the addition of other relevant information or examples of mutualism(lichen for example).

The section upheld a neutral tone throughout and did not try to establish its own conclusion. The author used their own language when presenting others' research. Improvements could be made in the languages. For example, by combining the second and third to last sentences to "In the case of siderophore secreting bacteria, sensing mechanisms has been adopted to adjust the secretion of siderophores depending on related neighbouring bacteria."

The 3 added citations came from reliable peer reviewed sources from established journals like the Royal Society. However, 2 of the papers drew conclusions that were not relevant to the statement of which it was cited to. The paper cited to insoluble iron was actually a neurological study on mice which was completely irrelevant to the topic. The statement about bacterial sensing is an unsubstantiated claim because the paper which was supposed to support it was actually supporting the previous sentence regarding the passage of similar genetic material, the paper itself did not make any discoveries about sensing. I would suggest for the author to find relevant sources to support those statements without literature backing. Aw13jcha (talk) 06:44, 9 November 2017 (UTC)