Naming policy

[David Goodman]

We can always add the categories--the first step is to decide how extensively to collect the names. I doubt it should be our intent to construct formal synonym lists in the accepted systematic biology fashion, or the multiple-language names that WP indulges in. I would certainly want to include the prinicpqal common names in use in English-speaking countries, and those names used in the recent literature--while recognizing that many readers will be accustomed to the considerably older scientific names found in textbooks.

[Derek Harkness]

Just to go on record as playing devils advocate before.

Scientific names are the only way to name and categorise these articles. For an example of the confusion and mess caused by common names, see http://pilot.citizendium.org/wiki/Grass.

Though I will remind people of my comments should I see an image captioned as "A young Acinonyx jubatus venaticus stalks a Gazella thomsoni through the tall Gramineae" (Yes I am aware of the geographical problems of the preceding.)

[Jaap Winius]

Why not include synonymy, with redirects even? Yes, it's more work, and it may not be all that important to people familiar with a particular taxonomy, but it can be very handy in a larger Wiki. For example, an ichthyologist may write "sometimes preyed upon by sea snakes of the genus [[Hydrus]],'' quoting some old monograph and blissfully unaware that this name has long since been changed to Hydrophis, but hoping that the name will later link somewhere. Without a synonymy and redirects, that would never happen. However, with a redirect (or disambiguation page) in place for this old synonym, Hydrus would link to something relevant right way. At WP, redirects for synonyms also prevent them from being used for other/new articles, although I expect that there will be less of that at CZ. Besides all of this, a list of synonyms often has an interesting story to tell from an historical point of view.

"A young Acinonyx jubatus venaticus stalks a Gazella thomsoni through the tall Gramineae".

Seriously, does anybody ever write like this?! 

[tkjazzer]

scientific names are essential to a good encyclopedia and I fully support a scientific naming system.  Redirects will solve any common name search problems.  Anyone who has studied chemistry understands scientific naming and its importance.  In anatomy, it is important to first learn the scientific name, and then if you are going in to surgery, learn the common ones as well since they still are used in the OR.  However, scientific name is the most important thing to learn first. 

Possible suggestion - add latin and greek roots to scientific names so that people see how these latin and greek names for biological things came about.

However, In general, the search engine needs improvement.

[Nat Krause]

Overall, I have no opinion about whether most articles involving organisms should use their scientific names.

However, I think that moving "Lion" to "Panthera leo" or "Horse" to "Equus caballus" violates the "principle of least surprise" to an unacceptable degree. Non-specialists are going to come to us looking for information on those subjects, and they will find it inconvenient to have the article located under another title. Perhaps there should be some kind of standard by which we can distinguish names that are in very common usage and that refer unambiguously to one animal. I don't know what such a standard would look like, though.

The second problem with using scientific names was alluded to by Derek Harkness and Jaap Winius. If we move the article on the Cheetah to "Acinonyx jubatus", are the authors really going to refer to it as such in the text? If not, what is the point of moving it -- we still end up having to settle on a common name to use in the text.

[Jaap Winius]

... I think that moving "Lion" to "Panthera leo" ... violates the "principle of least surprise" to an unacceptable degree. ...

This is a superficial way of looking at the issue at hand. The principle of least surprise may be good for some things, but if it were applied to everything science would never get anywhere. In this case it's being used to uphold cultural conservatism. The fact is, truth is strange and science is one long culture shock.

Of course scientific names look strange to most people -- most of them look strange to everyone! -- but that's not the point. Nobody is suggesting that CZ make any attempt to stop readers from using common names. It's just that there is no better way to organize thousands of articles on biological organisms. Also, by emphasizing them, scientific names are more likely to inspire people to learn things about the relationships between species.

Finally, let's not forget that, for the time being at least, CZ will be English-only, so it's possible that many English common names will be more confusing than scientific names to those for whom English is not a first language.

... If we move the article on the Cheetah to "Acinonyx jubatus", are the authors really going to refer to it as such in the text? If not, what is the point of moving it -- we still end up having to settle on a common name to use in the text.

Don't be silly. In my experience even the most hard-core scientific literature does not go that far when such a well-known common name is available. Perhaps we could come up with some guidelines for how to work with common names in the text and especially the introduction, but ultimately this is something that I think we should leave to the discression of the authors. The most important thing is that we agree on a single, clear, consistant and unambiguous standard for naming articles on biological organisms.

[David Goodman]

At least in molecular biology and kindred experimental subjects the common names are used throughout when there is a common name, though the scientific name is usually added somewhere in the abstract (If it's not there, Biosis tends not to notice it). This is sometimes done ambiguously--it can be difficult to figure out just what species of frog was used.

Even in other fields, even taxonomy,  in discussing a single organism the common name is generally used in the title if there is a common name (usually along with the scientific name). If a group of organisms is discussed in the article, the title is equally likely to say "bird populations" as "avian populations." To some extent, this depends on the nature of the journal.

I think this is enough precedent to say that the title should always be the common name if there is one, with the scientific name in parentheses. (And sometimes added without the parentheses, relying on the italics to make  the distinction).    Remember we are writing for generally educated laymen, and at least the identification of what the article is about should be accessible.  I would suggest that if there isn't one, at least the popular name for the narrowest group that has a popular name be added.

I am only discussing the title. To what extent we need uniform practices in the text is not obvious yet, at least to me--but it clearly is not quite as critical.

[Jaap Winius]

Here's a little demonstration of the practical advantage that scientific names have when it comes to managing categories. Recently, I finished adding category tags to all of the common name redirects, as well as the synonym redirects for the true vipers group. Here are the three main categories:

1. http://pilot.citizendium.org/wiki/Category:True_vipers  -  Valid scientific names
2. http://pilot.citizendium.org/wiki/Category:True_vipers_-_Common_names
3. http://pilot.citizendium.org/wiki/Category:True_vipers_-_Synonymy

1. is a list of the current valid scientific names according to the taxonomy I'm using. Most of these names are the article themselves, but a few (17%) are redirects for cases involving monotypic taxa and nominate subspecies. Except for those redirects, this is the shortest of the three lists and it's complete. It is also a well ordered list that specialists can use to tell what's here and -- more importantly -- what isn't.

2. is a list of all the common name redirects for the articles in the first category. Even though many of the species and subspecies in the fist category do not have common names, this list is much longer (over 200 entries). I've included all of the names that I know of that are used in the English language for the taxa in the first category. Mostly, this list is only of use to people who want to browse a list of common names, but at least at least it's relatively complete.

3. is a list of all the synonym redirects -- invalid scientific names according to the taxonomy I've used here -- for the articles in the first category. With over 500 entries, this list is nearly complete according to McDiarmid et al. (1999), missing only a few upper and lower case variants. If someone goes looking for a scientific name in the first list and sees that it is not there, they'll probably find it in this list (if not, it's probably very new, but may still be mentioned in a taxonomy subsection for one of the generic names). For people who are already familiar with many of the current scientific names, this list is kind of like a window into the past, showing the results of previous taxonomies as well as some proposals that may eventually be accepted.

If I were to use common names (where possible) for these articles instead, parts of the first and second categories would be mixed in with each another. To make the list complete, I'd really have to merge those two categories, but then you'd have a single main category with almost 350 entries instead of 133. Surly, this would be a step backwards.

Moving along, in response to those who still want to use common names for article titles, I say: argue the issues. Besides, if the articles are written like this one is...

http://pilot.citizendium.org/wiki/Vipera_berus

... with most of the common names listed clearly at the top of the page and with a picture of a specimen (well, there is at WP), how can there be any doubt what the article is about?

Finally, one of the things I'm worried about is that many of the specialist biologists that we would like to see writing such articles for CZ -- botanists, ornithologists, ichthyologists, mammalogists, etc. -- will be less than impressed if they see us following WP's naming policy. Taxonomy is very important to these people, at least to all of the ones that I've contacted, and I think it is likely that more of them will want to be involved if they see us doing things right this time.

[Larry Sanger]

Here's a little demonstration of the practical advantage that scientific names have when it comes to managing categories.

We may not have subject categories at all, except for workgroups and other administrivia.

[Jaap Winius]

We may not have subject categories at all, except for workgroups and other administrivia.

I'll be the first to admit that the use of categories at WP is way out of control, but isn't this a bit of an overreaction? After all, the three categories I've created (listed in my last post) are only different ways of looking at the articles, redirects and disambiguation pages for the same taxonomic group. The wiki system's category function is a powerful tool that does have its uses, especially when it comes to the many long lists of names that biologists are always having to deal with.

[Larry Sanger]

My question is: why is this better to do article-by-article, as you had to do (must have been quite painful), rather than all on one regular namespace page?

[Jaap Winius]

My question is: why is this better to do article-by-article, as you had to do (must have been quite painful), rather than all on one regular namespace page?

It isn't better. At least, it isn't better if you've already created all of the articles (or redirects) and have to edit them all again to add the right category tags. However, it is better to work this way if you plan ahead and add the correct category tags as you create the articles (or redirects).

Sure it wasn't easy to do what I did -- it took me about three days! But, I felt like I was on to something and wanted to see if it worked... and to prove a point (I hope).

[Larry Sanger]

Well, the Biology workgroup will have to address this question in general, and certainly the matter will not be decided based on the current disposition of some (excellent!) articles about vipers.  I say we can put off the question until January or February, when we're up and running more vigorously.

[David Goodman]

Back to the scientific terminology in the "arm" article. I cannot see a way to describe the arm without using these names for the structures. There are no common names for most of these.   Such a description never stands or its own: it needs to be accompanied by a visible diagram. and then it's clear. The text is not the important part in anatomy.

[Derek Harkness]

I think it's perfectly possible, and quite easy, to describe these parts of the arm without using so many specialized words. More so, I think it is an absolute necessity to do so. Here is one possible example of the same passage I quoted before but with a few extra words that change the paragraph from a name dropping exercise into something that might actually be useful. Simple additions like saying 'humerus bone' rather than just 'humerus'. The technical words are still there, but now you might understand them, just a little bit, without having to read a medical dictionary at the same time.

"Osteofascial compartments
The muscles in the arm are divided by a layer of connective tissue called 'fascia' (known as the lateral and medial intermuscular septa) which separates the muscles into sections called osteofascial compartments. One compartment to the front of the arm, the other towards the back. The fascia merges with connective tissue called 'periosteum' which covers the surface of the humerus bone. The osteofascial compartments contain muscles which are connected to and stimulated by the same nerve and perform the same action in controlling the movement of the arm."