Talk:Bioluminescence/GA1

GA Review

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

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Reviewer: Spinningspark (talk · contribs) 14:48, 9 December 2014 (UTC)

Lead

• The terms pigment luciferin and enzyme luciferase are both adjacent links to separate articles which is deprecated by WP:LAYOUT. In my opinion, pigment is a common enough word with a widely understood meaning that does not require linking. I suggest that the link to enzyme is moved to the next occurrence in the article.

Done. Cwmhiraeth (talk) 19:56, 15 December 2014 (UTC)

• • While on this issue, the same linking problem occurs in the body of the article. Also, the enzyme link is not at its first use.

Done. Cwmhiraeth (talk) 19:56, 15 December 2014 (UTC)

• On the other hand oxidation could be linked as this means something different from what people who don't know chemistry commonly think it means.

Done. Cwmhiraeth (talk) 19:56, 15 December 2014 (UTC)

• I think phyla is meant to come after groups rather than animals

Changed. Cwmhiraeth (talk) 19:56, 15 December 2014 (UTC)

• counter-illumination camouflage is another example of contiguous links. I this case the link to camouflage could be dropped as a commonly understood word.

Done. Cwmhiraeth (talk) 19:56, 15 December 2014 (UTC)

• Some fairly substantial sections of the article are missing from the lead: History, Distribution, and Biotechnology.

Added. Cwmhiraeth (talk) 20:25, 15 December 2014 (UTC)

Images

• File:Glowing tobacco plant.jpg is not a free image and does not have a fair use rationale for this article. Further, the article does not directly discuss this image, the experiment it came from, or even tobacco plants in general. Thus, an acceptable fair use rationale is going to be hard, or impossible, to construct.

If you look at the information about the image it states "Image taken by Keith Wood (of DeLuca lab) for Science Magazine. Permission to use on Wikipedia has been granted by Science Magazine (see talk)." I'm not sure what talk page is being referred to. Cwmhiraeth (talk) 19:56, 15 December 2014 (UTC)

Sorry, that is not good enough. While permission to use on Wikipedia from the copyright holder is welcome and makes it legal for us to use the image, that is meaningless in terms of policy. It is still in direct breach of the WP:NFCC policy and is therefore a fail of GA criteria 6a. It is also not showing an OTRS ticket number, so presumably the evidence that we have even this permission has not been sent in and is open to question by anybody. Ask on my talk page if you need further clarification. SpinningSpark 20:53, 15 December 2014 (UTC)

It's clearly unusable. Have described the research in text with the ref, image removed. Chiswick Chap (talk) 16:52, 16 December 2014 (UTC)

History and etymology

• The first sentence (on fish skins in coal mines) is an orphan (WP:LAYOUT issue) and seems decidedly out of place to the narrative. Perhaps it could be incorporated into another paragraph. Also, I am seeing several sources that describe the practice as "experimental" and not very effective, including these books [1][2], which is not really made plain. An indication of the historical period involved would also be good. Alternatively, expand the para with more information, there's a lot that could be said about coal mine safety and there is also this that says bottles of fireflies were used as well. This snippet names Murton Colliery "the most fiery on the Wear" (meaning most danger from gas) in connection with the use of fish skins.

Done. Cwmhiraeth (talk) 07:29, 17 December 2014 (UTC)

• "He refuted the idea that bioluminescence had anything to do with phosphorus". We seem to be missing the bit where someone claims it is to do with phosphorus.

Done; also added footnote - early modern (C17th) usage of 'phosphorus' did not necessarily imply the modern element.

• luciferin is not linked on first use in the article body.

Done. I'd like to leave the first usage in the chemistry section, it is the ideal place and "chemists" may not look at the history.

That's fine as a matter for editorial judgement. SpinningSpark 19:00, 16 December 2014 (UTC)

• "He sent Harvey siphons from the mollusc". If Siphon (mollusc) is meant here please wikilink it. If siphon is meant please explain exactly what is going on.

linked.

• The etymology sentence is an orphan sentence and a bit out of place with the rest of the material. I am guessing the only reason that the section is called History and etymology is to prevent the etymology being a one-sentence section. In my opinion, etymology is the business of Wiktionary and we need not include it unless there is something interesting to say about the history of the word. My recommendation is to ditch it. A sister project link to Wiktionary at the bottom would be enough. Besides, the ety is missing the -escence component of the word.

Ditched, it's not very exciting.

• Suggestions for possible expansion;
  • I recall Darwin in The Voyage of the Beagle describing bioluminescence on several occassions. That recollection is confirmed by this book search

Added a quote and some discussion.

• • Another recollection from dim memory is an anecdote by Chuck Yeager in his autobiography (which I thought was called The Right Stuff, but apparently that was by someone else) where he recounts trying to find his aircraft carrier in the dark with all its lights out for fear of being found by the Japanese. Yeager is saved by following a bioluminescent trail churned up in the wake of the ship which persisted for many miles. Apparently, this was a well-known trick, see this book search.

Added the Jim Lovell story (as a representative example, probably one of the more truthful!).

• • Also, the Economist article (your ref #47) has a discussion of wartime and cold war use of bioluminescence.

OK, done that too. That makes the history quite long enough for the article.

Chemical mechanism

• The chemical formula contains a lot of components that may well not be familiar to the general reader and should by defined. I am familiar from physics with the symbol \nu being used for frequency and instantly recognise that hν represents a quantum of light through the relation with Planck's constant, but even to an electrical engineer that might be a bit obscure where f is expected for frequency. It is an item especially in need of explaining as it is a slightly unusual thing to write in a formula; even many textbooks just write "+light". Other items you might want to explain are that L stands for luciferin and the meaning of the suffix i on PP.

Clarified/replaced symbols.

• C02 is a typo

Fixed.

• Lux operon is incorrectly capitalised

Fixed.

• "nine phyla (ancient groups...)". Phyla does not mean ancient group. This should be rephrased perhaps something like "nine ancient phyla..."

Done.

• photoprotein aequorin contiguous links

Fixed, didn't know it was a problem.

It's in MOS/LINKING, and was in WP:LAYOUT, which made it a GA issue, but was removed from that page !today! as redundant to other MOS pages. So strictly speaking, it is no longer a GA requirement (unless it gets put back in). SpinningSpark 19:19, 16 December 2014 (UTC)

Distribution

• "as well as some bacteria". This is a repetition already in previous sentence. Suggest merging the link into the first mention. By the way, fungi could also be linked to List of bioluminescent fungi.

Done.

• "the wavelengths that pass furthest through seawater". I am not seeing this in the paragraph cite so assume it is uncited. This book tells me that (a) it is not that simplistic, varying considerably from ocean to ocean, and (b) that except for the central Pacific green is absorbed significantly less than blue. Minimum light absorption in the Baltic is even in the yellow band according to their graphs. The graph in this book more or less agrees with that. It shows that pure sea water has a sharp minimum attenuation in blue light, but the curve of the effect of impurities is going to shift that towards longer wavelengths. The table on the next page again confirms that there are large differences between oceans.

Removed.

Use in nature

• "burglar alarm". Does that mean to warn other individuals?

Said it's to make predators more visible to *their* predators.

• "sacrificial tag". Now I was just reading what that meant a moment ago, but I can't find it in the article so I guess it wasn't there

Removed, it's only anecdotal, says Haddock.

Attraction

• Fungus gnat should be wikilinked

Done.

• "emits the bluest light of any known insect species" Not seeing that in the source.

Done.

• "The attraction of mates is seen actively in fireflies." That could be written better.

Done.

• "emit an orange light from the abdominal when flying" That should either read "from the abdomen" or "from the abdominal <foo>".

Done.

• Can we reword to get rid of the WP:SCAREQUOTES in "luminous termite mounds"?

Done.

Defence

• Is it really necessary to use the jargon "spp."? Could we say "Genus Phrixothrix" instead? Or if you just mean some species of the genus, then say that.

Removed.

• "The function of these may be in the detection of their millipede prey". Not clear how this is meant to help detect millipedes. Is it just for illumination? I would have thought that the shorter wavelength green light was more suitable for this.

Removed, it seems no more than a guess by the scientists involved.

Communication

• "Communication (quorum sensing) plays a role..." Quorum sensing does not mean communication as the brackets would seem to imply. In fact, the word communication is redundant as the section title already tells us that is what this section is about.

Clarified.

• Presumably it is high messenger molecule densities that trigger the light to come on. The creature is not directly aware of the population density per se.

Clarified.

• "to attract prey" > "to attract them as prey"

Done. (Said "to attract its males as prey". Other usages of the phrase are correct.)

Defensive mimicry

• The only example given is a cockroach that is not even certain uses light at all. The reader might be forgiven for doubting that bioluminescent defensive mimicry exists at all. However, the book Bioluminescence: Fundamentals and Applications in Biotechnology vol.1 introduced me to the term Batesian mimicry (which should probably be linked in the article) on which they have a section, and suggests there may be more information to be had. However, if this is all there is, then the article should be much more circumspect in what it claims about mimicry in the lead and introductory paragraphs, or even drop the claim altogether.

Added more information and removed subsection headings. Cwmhiraeth (talk) 07:04, 17 December 2014 (UTC)

Illumination

• I had to read the description of the black dragonfish's eyes several times before I understood it. Both sentences are trying to say too many things and need breaking up into simpler statements.

Done.

Biology and medicine

• Vibrio has already been linked previously

Unlinked, but I wonder if this slight overlinking isn't desirable here.

Repeated links are fine if you have a good rationale for doing so, at least as far as GA is concerned. Of course, you will have to guard the article forever against wikignomes trying to remove them again. SpinningSpark 20:36, 17 December 2014 (UTC)

Light production

• "...in a bio bulb." I think we need to explicitly say "light bulb" to avoid misunderstanding, and possibly wikilink it.

Done.

• iGEM should be wikilinked

Done.

External links

• This seems slightly overstuffed for a GA. The UCSB site seems particularly uninformative and could go.

Done.

References

• The references are quite variable in their quality. There are a couple in particular that are borderline reliable. Not so bad that they have to be replaced, but worth looking to see if something better could be found.

Ok

• • Ref #1 [3] is from a site selling replica miner's lamps. The article is uncredited and there is unlikely to have been any peer review.

Removed.

• • Ref #22 [4] is an article from h2g2. First of all, the page has been retrieved from the BBC website, but the BBC no longer maintain h2g2. The page appears to be left over debris from the BBC discarding this enterprise and many of the links no longer function properly. The active page is now here. More importantly, the material is user submitted in a wiki-like environment from users identified only by username pseudonyms. There is a peer review process, but it is through other users of the site, so it is dubious that this counts as reliable.

Removed, rewritten using Haddock's review paper.

• Ref #33 does not give the journal name. The convenience link requires login which makes it fairly useless. However, the full text seems to be available here so I suggest that is used to replace the link.

Done.

• SpinningSpark 01:39, 15 December 2014 (UTC)

Thank you for taking on this review. (Is your spinning spark of biological origin?) Cwmhiraeth (talk) 19:56, 15 December 2014 (UTC)

Re username, no, I had skating electrical engineer in mind when I chose it, but it really doesn't mean anything. Or are you asking if I am human or machine? SpinningSpark 20:57, 17 December 2014 (UTC)

Many thanks for the careful review. Chiswick Chap (talk) 10:04, 18 December 2014 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.