User:Polypompholyx

In real life, I'm Ste Cook, currently earning a living at Imperial College London, teaching biology. I tweet, and blog as Polypompholyx. I am interested in Perl, botany (especially carnivorous plants, pine-cones and plant phylogeny), and public engagement with science, although from the majority of my edits on Wikipedia you might think all I do day-in-day-out is go round looking for unitalicised Latin names.

Science Communication Wikipedia projects
As part of the Science Communication module for final year Life Sciences students at Imperial College London, a group of students select Wikipedia articles to improve. They mostly select stubs, but some select more substantial articles: some of these were suggested by staff in Department of Life Sciences as being in need of updating, referencing, or review. Prior art is listed below: most of the articles are improvements on what was there before, although a few - unfortunately - were not. Most of them have been edited (often by me) after the event to address the main issues I and other editors noted.

I hope that overall this has made a positive contribution to Wikipedia, but I'm very happy to have feedback on my Talk page about this. Some of the more substantially improved articles are N-linked glycosylation (which was previously extremely incomplete for such an important topic), the taxa Ugandan red colobus and rufous fantail, the protein SIGLEC, the article on progeroid syndromes (contributed by a student who was already a somewhat experienced editor), and the article on gas exchange.

Unfortunately, this project ran for the last time in March 2020: the articles were sumatively assessed as part of student coursework, and this became increasingly difficult to do fairly when students were mostly improving existing articles rather than creating new articles from scratch. I would like to reinstate this as a formative exercise in future, but the last few years have been extremely difficult and I'm not sure when, or if, I will find the time to do this.

Instructions for students 2020
Please edit the 'List of student editors' subsection below to add yourself to the project. Use the [edit] link next to the 'List of student editors' subheading below, to avoid any possibility of trashing the rest of this page! You need to include:


 * Your name (optional). This doesn't have to be your real name if you don't want to put it here (just use your editor name instead), but you'll need to email me instead to let me know who you are if you want to be (pseudo)anonymous.
 * A link to your User page. Just type four tildes (that's the ~ sign) to automatically insert a link to your User page and Talk. I'll edit away the time-stamp later. Your editor name must not be your College username; and your password for the Wikipedia account must not be your College password.
 * Your proposed article. If your article doesn't exist yet, don't create it with blank content, because it will be speedily deleted. Create a dead link in the list below to the Article that is yet to come, and then write the new article in your Sandbox. You can create the article itself once you have a substantial amount to contribute, or you might consider using the Drafts feature. If you do create a new article, make sure it is added to any relevant Categories, and that you link to it from at least one other relevant article, so the article is not an Orphan.
 * You will also need to let me know by email the name of a person you have approached as a 'content' second-marker if the article is on something obscure. I will mark the Wikipedia aspects of the article, but I can't know everything about the biology/biochemistry itself, so you need to find someone on the staff who can comment on this. Please make sure you have emailed them to ask if they would be prepared to do this: if it comes as a nasty surprise when I come to ask them for marks, then you will not have met the broadly applied 'be civil' criterion. If you are having to find an expert marker, this may well indicate that you have chosen a topic that is of narrow interest. Think very carefully about whether you would be better of attempting one of the hand-selected suggestions listed below instead.

List of student editors
Add your details to this bullet pointed list. If this raises an anti-vandalism error, put your details on my Talk page and I'll transfer them across.


 * e.g. Ste - Polypompholyx (talk) - Carnivorous plant

Choosing your article
Here are some pages that you should consider editing. I will consider your own suggestions, but any article you select yourself needs an expected audience much larger than just you, me, and the second-marker. Consider quite broad topics of interest to a general science audience (consider A-level specification topics, or the topics of substantial pieces of the early part of your degree); or, if the topic is more specific, make sure it's important (model organisms, invasive species, enzymes of central metabolism, important receptor molecules). Read the article on gas exchange as a good example of what you can bring in terms of accessibility, clarity, and technical detail to an article on a general topic: it's not perfect, but it's very more the kind of topic I want you to approach: not a monograph on a very obscure taxon or protein.

Whatever article you choose, it must be written as accessibly as possible. In particular, the lead section should be as clear as you can possibly make it, and understandable to - at least! - a first-year undergraduate student.

• Bohr effect and Fetal hemoglobin - Neither are very accessible or well-illustrated for articles that are staples. Requested by a teacher.

• Coralloid root - The roots of cycads can develop into nitrogen-fixing structures at the soil surface containing cyanobacteria - photographs could be obtained from a trip to Kew.

• Denitrification - Ecological and agricultural importance? Bacteria and metabolic systems involved?

• Electron transport chain - Quite a lot here, but it's not very well organised, and very badly illustrated. Some consistent diagrams and better pitch would be helpful. Could also include material on ETCs in bacteria, reverse-electron flow. Requested by a teacher.

• Genetics of maize - There's a good book in the library on this, and we also have cobs you could photograph.

• Loop of Henle - Kidney function article: poorly illustrated and jargon-y. Suggested by a teacher.

• Monosaccharide - Text is better than it was, but still quite poorly illustrated.

• Nearly neutral theory of molecular evolution - Lead section isn't very accessible, few references, examples, comparison to neutral evolution.

• Nicotiana benthamiana - Important model organism, some staff here work on it.

• Nitrogenase - Some recent improvements, but needs editing to bring the raddled ragbag of information together into a coherent article.

• Notch_signaling_pathway - Needs diagrams

• Plant tissue culture - Could do with more illustration, updating, and relevant material about manipilating hormones for callus production. Suggested by a teacher.

• Retrotransposon - Rammed with jargon. Links to lots of child-articles, so this needs to be a high-level, accessible overview. Illustrations? The child-articles (e.g. Short Interspersed Nuclear Elements (SINEs)) are similarly poor.

• Secondary metabolite - Basically just a list. Rewrite as an article with examples, illustrations of the chemicals and plants.

• Signal crayfish - Serious invasive species. Silwood Lake is full of them.

• Stele (biology) - We have lots of slides you could photograph for this.

• Sphingobium chlorophenolicum - The bug that breaks down PCP from the practice exercise. Read the Copley paper!

A larger list of biology and ecology topics may also be a useful place to look for inspiration, particularly those tagged for Clarity or Content issues. These were provided by WikiMedia UK, to whom I am greatly indebted.

Editing your article
Articles need to conform to the Manual of Style - in particular:


 * Articles must have a title (obviously!) In some cases, this needs to render in italics, because it is the name of a gene or a Latin binomial. Make sure it does if it needs to.
 * Articles must have a lead section. This should give a highly accessible overview of the whole article. It should be understandable to an interested lay audience. Do not cram it with jargon. Make sure the first use of the title and any synonyms of that title are in bold. I often see editors including jargon words and phrases in the lead which link to (and are) the titles of articles. The obvious intention is for the reader to click on the link, so they can get an explanation of the jargon word. Unfortunately, that just leads to a jargon death-spiral when it turns out the linked article's lead is also crammed with jargon. You need to short-circuit this. A simple way to do this is to do this kind of linking 'inside-out': link to the jargon word's article, but through a longer piece of text that explains the jargon directly. Rather than saying "Cell adhesion can be involved in signal transduction", say "Cell adhesion can allow cells to detect and respond to their surroundings".
 * Use sections and subsections to break up your text, but remember that this is an encyclopaedia written in prose, not a shopping list written in bullet-points: over-use of subsections can make an article extremely bitty.
 * Your article must be properly referenced so the article will meet the Wikipedia Verifiability criterion. The Cite DOI feature in the VisualEditor is extremely useful for this, but make sure you curate the reference after inserting it: italicise Latin names and gene names, remove extraneous date material (it's usual for references in scientific articles to contain just the year of publication, not the entire date), and make sure the item is complete (author, year, title, journal, volume, pages, plus the DOI if it has one). You know what you should be doing, as the library taught you how to use RefWorks: the same applies here as for any essay. Using primary literature is OK, but an encyclopaedia is really tertiary literature, so should be presenting a high level summary of secondary sources (i.e. good text books, review articles, etc.), not delving into excessive detail from primary sources, so I suggest you take a look at books in the library, not just search WoS. The same rules apply as always for citing websites: generally avoid it, unless the source is known to be reliable, e.g. NCBI, PDB, etc. One additional thing to add to your references' ref tags is a name attribute, to make the reference more easily reusable: I'd suggest using   (e.g.  ) consistently.

Being civil
You should also add the following tag to the Talk page of the article you want to edit to mark it out as an educational assigment:



It should render like this once you have (previewed and) saved the Talk page:

Also briefly introduce yourself on the Talk page of the article, explaining your intentions and the main things you want to do to the article: this will help you avoid editing conflicts. If you create an article from scratch, make sure it has the educational assignment tag added to its Talk retrospectively. Be mindful of the additional community standards of any WikiProjects that your article belongs to, especially WikiProject Medicine.

You must also write a brief biography on your User page explaining why you are here: this can be (pseudo)anonymous so you don't need to include any personally identifiable details. However, the fact you are a final-year life sciences undergraduate at Imperial College will be obvious from your activity: if you are uncomfortable with that information being public, then please speak to me in person and we'll make some arrangement.

A picture tells a thousand words
In previous years, students have often focussed on adding a lot of text and references to articles. I don't particularly want to discourage this, but better Wikipedia articles will also be well-illustrated. Sometimes you will be able to find good illustrations on Wikimedia Commons, or be able to modify diagrams you find there (for e.g. species distribution maps).

However, you are strongly encouraged to make and upload your own diagrams as well: these can be made using tools you are familiar with such as PowerPoint, PyMOL, R, or by learning how to use other graphics programs (e.g. vector-based Inkscape, or raster-based Paint.NET). Many articles would benefit from good phylogenies: these can be made using the cladogram template in a format that other editors can later modify - this is far preferable to including difficult-to-edit images of phylogenies. I have a Python script that can convert a simple mark-down like:

-Embryophyta -Liverworts -_____     -_____        -Hornworts -Tracheophytes -Euphyllophytes -Spermatophytes -Gymnosperms -Angiosperms -Ferns -Lycopods -Mosses

to the clade format that will render as shown below. This is available on Blackboard.

Any diagrams you do use (or create) must be free, i.e. licensed by the creator (which may be you!) using Creative Commons. Other useful templates are taxoboxes and protein infoboxes.

In addition to making your own simple diagrams, the Department has materials you can photograph or use that might be relevant:


 * A huge microscopy slide collection (10000+): I have a detailed index for this collection, so just ask me for it if you're looking for sliced-and-diced parasites, plants, etc.
 * A large collection of mammal skulls (50+) and of pinecones (100+).
 * All of my lecture PowerPoint slides from first-year are CC-BY-SA, and you're welcome to use and modify any of my self-penned diagrams. I also have several template PowerPoint and ChemDraw files of molecules, organisms, membranes, cells, metabolic pathways, and similar that I'm happy for you to use: just ask.

Diagrams are important, but may not be accessible to those with visual impairments. Please consider those with colour-blindness - particularly avoid meaningful red/green colour contrasts unless there are other cues (shape, dotted/dashed lines, etc.) that help distinguish items; and avoid black-text-on-red-background (and vice versa) altogether. All images should have captions, but for those who are viewing Wikipedia with a screen reader, make sure that images also have an alt text that goes further than this: it doesn't have to literally describe every last thing in the diagram (although it might), but consider whether a person who will never see your image will still be able to understand what it shows from the alt text you write for it.

Science Communication Wikipedia project 2021
• Unfortunately not able to run due to COVID

• Cycas thouarsii - I did a fair amount of work on this article, so including it as an honorary!

Science Communication Wikipedia project 2020
• Artificial gene synthesis

• Community (ecology)

• DNA synthesis

• Emergent virus

• Fetal hemoglobin

• Host switch

• Hypersensitive response

• Innate lymphoid cell

• Ophiocordyceps unilateralis

• Pichia pastoris

• Protein biosynthesis

• Pyroptosis

• Respiratory burst

• Retrotransposon

• Secondary metabolite

• Symmetry in biology

• Ti plasmid

• Transplastomic plant

• Viral pathogenesis

Science Communication Wikipedia project 2019
• Designer baby

• Mitochondrial theory of ageing

• O-linked glycosylation

• Pseudopodia

Science Communication Wikipedia project 2018
• Active site

• Cell adhesion

• Cline (biology)

• GSDMD

• Hapten

• Intravital microscopy

• JAK-STAT signaling pathway

• L-arabinose operon

• Xerophyte

Science Communication Wikipedia project 2017
• Eimeria

• Gas exchange

• Solenoid (DNA)

• Onchocerca volvulus

• Immobilised enzyme

• Phagosome

• Single-cell transcriptomics

Science Communication Wikipedia project 2016
• Black Colobus

• Cape mountain zebra

• Caspase

• Endangered species recovery plan

• Mixed acid fermentation

• Fasciola hepatica

• Nitrogenase

• Phylotypic stage

• Raitt's sand eel

Science Communication Wikipedia project 2015
• Akt/PKB signaling pathway

• Alphabody

• Amniotic stem cells

• Ball and chain inactivation

• Cav1.3

• Importin

• Flux (metabolism)

• Mothers against decapentaplegic homolog 4

• Nectarivore

• Regeneration in humans

• RNA-induced silencing complex

• TFIIB

• Transcription factories

• Type 2 secretion system

• Type VI Secretion Systems

• Universal Stress Protein

Science Communication Wikipedia project 2014
• Bdelloidea

• BioBrick

• Chaperone-Usher fimbriae

• Echinostoma

• FADD

• Granzyme B

• Gut specific homing

• Intraspecific competition

• Lantana camara

• Mannose 6-phosphate receptor

• Mannose receptor

• Northern Sportive Lemur

• N-linked glycosylation

• Osteochondroprogenitor cell

• SCN10A

• Thioester-containing protein 1

• Ventrolateral preoptic nucleus

Science Communication Wikipedia project 2013
• Active site

• Ancylostoma caninum

• Bacterial display

• Banana Xanthomonas wilt

• Carnassial

• Chromothripsis

• Cicindela dorsalis

• Gas exchange

• Equine encephalosis virus

• Galectin

• Glis1

• Key innovation

• LGR5

• Lutzomyia

• Mokola virus

• Photorhabdus

• Progeroid syndromes

• SIGLEC

• TIGAR

• Xenoma

Science Communication Wikipedia project 2012
• Acrogeria

• Canarypox

• Cre recombinase

• Density dependence

• FDC-SP

• Granule cell

• Grb2

• Human parainfluenza viruses

• Hypnogram

• Metrioptera roeselii

• Natural killer cell

• Parasitic nutrition

• Phymatopus

• Pyocyanine

• Pyroptosis

• Rufous Fantail

• Trophic egg

• Ugandan red colobus