Monday, March 14, 2011

Taxonomy in the News: Taxonomy, the naming crisis

It is always a good thing to be covered by the news, so no complaint about today's article about taxonomy in the Independent.

Besides that, it is as usually depressing to read a necrology of a science that seems one to make the news with morbid reports, such as the decrease of taxonomist, the increasing underfunding, the lack of universities training taxonomists.

There is so much happening in and around taxonomy, but the speakers for taxonomy seem to be conditioned to mourn and black painting, complaining about the technophile funders. A little bit more creativity and optimism in communication of our science would not do any damage.

Sunday, March 06, 2011

Global Names Index (GNI)or don't we learn anything?!

The other day I was looking up Panacedechis papuanus trevorhawkeswoodi on Google to see what is known about this species and whether I can find some images. What I found was the link to the Global Names Index, I guess, because there is not so much online on this particular species.
What frustrated me immediately is, that there are just name strings. Names attached to nothing. Not even an author. And then there are name strings with an author and year, but they are not linked, not reference given, and when one clicks to the source, it is just a dead end without actually displaying the citation.
I think this is incredible for a new tool that wants to deal with all names, and is supported by the Global Biodiversity Information Facility (GBIF). We don't know what's behind a particular name in a particular publication. But now, we do not even now to what use of the name refers.
I always hoped, that especially institutions like GBIF, one of the main player in the field of biodiversity informatics, would push that names are linked to a publication in which links are provided to the materials examined that allows to understand the species concept used in this particular usage.

But no, they seem to be even more ignorant of what the Internet provides: Linkage.

I am hoping, I am wrong.

Saturday, March 05, 2011

Makham, Hawkeswood and Calodema: What a strange set-up

The journal Calodema has become the red herring in taxonomic publishing because of the very low standards of its publications. The editor of Calodema, Hawkeswood seems to be a very competitive fellow as is seen in this exchange from one of his papers, commenting on two letters that Chadwick mailed him:
I do not need to say much more and I will now continue with publishing papers overseas in entomological journals, without worrying any further about C.E. Chadwick and his cronies. Into the dustbin of history he and his research go!
The current debate in the Taxacom listserver refers to a very recent description of a new spider family, the Hawkeswoodidae Makhan & Ezzatpanah published in A new spider family, Hawkeswoodidae fam. nov. and Amrishoonops amrishi gen. et sp. nov. (Araneae) from Suriname; however, when opening the link, a different paper appears "Aschnaoonops aschnae gen. et sp. nov. from Suriname (Araneae: Oonopidae)".
But then, as Thorpe points out
Hawkeswoodidae was proposed with Amrishoonops as type genus! As it is not formed from the stem of an available generic name, it is not available [sensu ICZN be a noun in the nominative plural formed from the stem of an available generic name] ...

When you actually read through the description, it is extremely short and makes no mention of why this species and genus is different from any existing one.
Description (male): Total length 1.8 mm. Palp with a C-shaped projection. Underside of projection strongly sclerotised, upper side soft, open and seed-like inside. Palp with large brown setae on dorsal side. Carapace brown, with brown setae, widest at posterior side. Abdomen on dorsal side light brown with brown setae, ventral side brown, with brown setae. Spinnerets light brown, with white setae. Legs light brown, with white hairs and with large thick spines.

and here the generic description

Type species: Aschnaoonops aschnae Makhan & Ezzatpanah sp. nov.
Description: Small brown species. Carapace round. Palp with a C-shaped projection. Underside of the projection strongly sclerotised and upper side soft, open and seed-like inside. Legs with large thick spines and hairs.

May be such as simple description is like Einstein's E=mc2, we just don't get it - that at least seems to be the message at the main page of Calodema
"All truth passes through three stages: first, it is ridiculed; second, it is violently opposed; third, it is accepted as self-evident!"
- Arthur Schopenhauer

"Great spirits have always encountered violent opposition from mediocre minds."
- Albert Einstein

P.S. Looking at some additional publications, it seems that Calodema is in fact the journal for highly combative authors, like Ghahari in his checklist of Iranian Braconid wasps
The results of this research indicate that the braconid fauna of north-western Iran is diverse and comprises some very interesting species. The mentioned region is very vast and includes diverse flora and fauna, and also has boundaries with Turkey, Armenia and Azerbaijan. Therefore, this small research paper, which is restricted to some areas, is not an extensive work, and the conducting of other surveys is necessary for determining many other species in this region. Since Iran is a large country with various geographical regions and climates, faunistic surveys in different regions of Iran is necessary for determining the extent of Iranian Braconidae step by step. A checklist of Iranian Braconidae was published by allahzadeh & Saghaei (2009) without perfect attention to all the resources available on Iranian Braconidae, e.g. Ghahari et al. (2009a, b, c, d) and many others. A checklist is a type of informational aid used to reduce failure by compensating for potential limits of human memory and attention.
Therefore, it is expected that a checklist would contain all the data on the subject and a checklist with deficiencies is not usable and helpful for researchers. This is main reason that all the systematic checklists must be prepared by the authorized specialists or at least edited and/or refereed by them carefully.
Caught in your History, marred in Garbage

Eli Pariser made a plea at his Junk Food Algorithms and the World They Feed Us TED lecture to Google, Facebook and other social networks not to cage the users (all of us) into their own history, and essentially make them unaware of different opinions.

This is similar to an analysis of Ghaddafi and his peculiar style of dressing and acting: Nobody does tell him anymore, that this or that might be questioned.

Whilst doing so might end up close to capital punishment, Google et al seems rather stuck in a wrong philosophical approach, that somebody can be defined by few mouse clicks.

I would argue even further. Google not only puts on blinds on my eyes, it is mainly garbage that I am being fed. Most of what I really want does not show up, because the algorithms operate without context.

For example, if I want to know something about "Formica" a group (genus) of ants living in the northern temperate region, I get Formica as material but furthermore a huge array of pages that somehow end up to have Formica in them ("About 6,770,000 results").

Does this make sense? Google is the victim of its own success, and I think a very stubbern company with the same symptoms of all the succesful companies: Becoming stupid because of the insistence of its own past, the search algorithms, web crawlers and server capacity to was at the begin of its success.

So, what is missing here is context in the search.

And this might not be just Google's mistake. As long as we stick to context insensitive html, we do not deliver Google the "Food for search" they need.

Alas, we need to move into the semantic tagging of content - and that's where I believe lies the success of our approach to add domain specific elements to publishing XML, such as the NLM Journal Archiving and Interchange Tag Suite, which then becomes TaxPub, which now is used by Pensoft with all its advantages of dissemination its content as widely as possibly, and being harvested. Such a small harvester is Plazi, that allows searching within the contest of treatments (the descriptions of species, such as species of Formica) or other elements that have been tagged, resulting for example in a list of species of a particular country