Category Archives: Ichthyology

Vandals in Nomenclature?

The discussion recently in the iczn-list (yes, an e-mail discussion about matters related to the International Code of Zoological Nomenclature) has been heated by vandals. That is, strong feelings have been expressed about vandals in taxonomy.

The reason there are vandals is because there is a definite ethically correct behaviour in matters nomenclature, and because Zoological Nomenclature is one of the oldest and best functioning globally endorsed anarchistic systems in history. There are rules, but it is up to the users of names to follow the rules. Strangely, it works most of the time. Vandals are those that do not follow the community rules, but abuse the system, taking advantages they should not have. Abusing freedom is inviting control. And that may not in the end make the world better.

Taxonomic vandals are of a few different kinds (my classification).

(1) Hooligans. These folks are absolute nuts about publishing new names. Whether their species exist or not is irrelevant to them. In the most recent example discussed, author A published a description of species B, and then copy pasted the same description for species C. This seems to be a pest among herpetologists and malacologists.

(2) Nominomaniacs. Nominomania is the obsession with scientific names, which in itself is possibly harmless, but there are bad guys (men only) here. Nominomaniacs of the bad kind eat homonyms like caterpillars chew leaves. They make new names for every junior homonym they can find, without checking up the organism, or whether a specialist may not already be concerned with these homonyms. Nominomaniacs are frequently authors of names outside their group of speciality, if they have any.

(3) Mihi-itchers. These people cannot leave any variation in nature without a name. Somehow they also frequently happen to publish a first name for the same species as a colleague is working on. A special case of advanced mihi itch is the Phylocode where you have to put a new name on every clade you may happen to find (I am provocative here). Mihi-itchers, like sneakers, lurk among the posters at conferences, take photos, and save many days of work efficiently and conveniently.

(4) Sneakers. Whenever a specialist has established a descriptive standard for a group, sneakers will copy paste his/her descriptions, make a few changes and apply it on their own species, preferably ones that are already under study by a specialist. Aquarium hobbyists do this, because they have no training in ichthyology and do not know what they are looking at. Students may be tempted to take this easy road as well.

They are not many, maybe 10 or so in the world at any given time, but they upset people considerably. You know these persons because they as a rule do not participate in scientific meetings, usually run their own journal or exploit weaknesses in journals that do not have a strong editorial control, have no research funding, always have specimens from places where nobody else gets a permit to collect, etc.

Why is it so? Taxonomy has no impact factor of interest to society or funding, so why bother?. Psychological factors aside, Nomenclature has one major problem called authorship. It is more or less obligatory to put the name of the person(s) who described a species after its scientific name.

Consider Dicrossus filamentosus (Ladiges, 1958).

Ladiges did a not very good one on this species; it was published as a sort of preliminary description in an aquarium magazine, based on two very dead aquarium specimens without locality, described by a non-specialist. It is a distinctive species, so no real harm done, and there were no specialists on South American cichlids available at the time. Most of the relevant information about the species, including geographical provenance only appeared with my redescription in 1978 (a student paper, not so advanced, but still helpful). Ladiges will forever be cited as the author of the species, although he did not do anything useful with it. Later workers will be more helped by Kullander (1978), which is practically never cited.

I take this particular example to show that even if the scientific basis for a description is very, very weak, it frequently gives more citation and more food for the ego than any other work on that species later. Confounding authorship associated with scientific names with scientific citation is bad in itself, but it also certainly is a major driving force in taxonomic vandalism.

In science elsewhere, bad or boring (like taxonomic papers) papers never get cited again, and their authors are peacefully brought to oblivion. The only way outside taxonomy to obtain a reputation is to work hard to do something useful.

The end result is that we have an extra number of useless names that specialists must consider for the rest of their professional career; we have lots of duplicate work, blocked access to relevant specimens, type specimens deposited in private collections unavailable to specialists, loss of trust in the profession, and in the end uneasiness and unwillingness among professionals to communicate openly about their work.

The Code of Ethics in the International Code of Zoological Nomenclature, is very straightforward about what behaviour is expected from those making nomenclatural statements. In the case of my lab, we work on the systematics of danionine cyprinid fishes, the genus Puntius, South American cichlids, and in collaboration the fishes of Myanmar and Paraguay. I am not expected to check with others whenever I have a new species in these groups, and there are many of them. Everyone knows that we work on these fishes (or would have known if the Newsletter had existed; see previous blog). You do not have to check with me if you are thinking of describing a new species of goby from the Seychelles. But if I would find a new goby from the Seychelles I would need to check if somebody else might be working on it. And anyone working on any of the above groups is expected to check with me first, and with other colleagues that have known interests in the same area.

Two weeks ago I received a new species of fish; concluding it was new and interesting enough to describe, I checked with another specialist on that family two days ago, and it turned out he has the same species from the same place, so we have to make an informed and friendly decision how to go about it.

The job of the taxonomist is to a large extent to give scientific names to organisms. It is a little reward on top to the sometimes repetitive analytical work. Of course, we all get a little of the mihi itch (mihi means mine; this itch is about appending one’s name to species names), but it easily cured. However, among the many, many scientists in Ichthyology that I respect, all of them were always more concerned with the analysis than with their author status, and more concerned with having a publication that people want to read and use, than having their names cited. That is what science is about.

So, what should we do? Outlaw some people or journals? Permit only certain journals to publish nomenclatural acts? Apply to the Commission for suppression of every name not considered appropriate for whatever reason? Ignore the names published by vandals?

In the end, who judges vandalism? When am I a 100% vandal, or a 10% vandal or perfectly non-vandal, in the eyes of 5%, 50% or 100% of my colleagues? Is this about people or about the Code? Who is more mihi-itchy at the end of the day, the vandal or the vandalised? Ethics cannot be ruled, it can only be demonstrated. So, I would prefer to leave the system open, with the very slight disadvantages it may have. But the Code of Ethics of the International Code of Zoological Nomenclature maybe should be more widely known.

What does the Zoological Code say then. I quote the most relevant parts of the Code of Ethics from the ICZN website:

1. Authors proposing new names should observe the following principles …

2. A zoologist should not publish a new name if he or she has reason to believe that another person has already recognized the same taxon and intends to establish a name for it (or that the taxon is to be named in a posthumous work). A zoologist in such a position should communicate with the other person (or their representatives) and only feel free to establish a new name if that person has failed to do so in a reasonable period (not less than a year).

3. A zoologist should not publish a new replacement name (a nomen novum) or other substitute name for a junior homonym when the author of the latter is alive; that author should be informed of the homonymy and be allowed a reasonable time (at least a year) in which to establish a substitute name.

4. No author should propose a name that, to his or her knowledge or reasonable belief, would be likely to give offence on any grounds.

5. Intemperate language should not be used in any discussion or writing which involves zoological nomenclature, and all debates should be conducted in a courteous and friendly manner.

6. Editors and others responsible for the publication of zoological papers should avoid publishing any material which appears to them to contain a breach of the above principles.

Some interesting examples where opinions are strong:

Adamas Huber 1979 replaced by Fenerbahce Özdikmen et al. 2006

What herpetologists talk about

Where are the ichthyologists?

I have admired some MySpace pages by non-ichthyologist colleagues, complete with all personal data, list of publications, etc. They remain there even after said colleagues have moved from the address they left there. Maybe MySpace is not their or my kind of space.

I tried LinkedIn, which is a community for mostly business people, but does not offer much of services. There is a lot of people there that I know, but not much I can do except have the contact details up, and wait for a chain of contacts to grow. It says that I am linked to 33 900 other professionals. I do not know if that is good or scary, but it is more people than I know personally.

FaceBook is fun, and promises plenty. It seems to be a place where a few wrong clicks can open you up to the whole world to come say hello to you. That is not really my idea, as I am quite non-social in a way. FaceBook is not a professional meeting point.

Wait a minute, there was a community for systematic ichthyologists! It was the Newsletter of Systematic Ichthyology, which was published as xerox copies by Bill Eschmeyer and ichthyology staff at the California Academy of Sciences, largely handmade I understand. You had to send in a formatted resumé of what you “are doing now” (before Twitter …) and CAS colleagues formatted and sent it out. It was very helpful and spared you time and money otherwise to waste on going conferences. Helpful because you learned about what people were doing so you could avoid doing the same, or contact them if there seemed to be some interesting information around.

The Newsletter then was acquired by a project called DeepFin, which was about collaborative molecular fish phylogenies. And with that the collaborative newsletter disappeared in some cybervacuum.

And yesterday, I found the solution, which this time was not an ichthyological invention, but seems to be the platform we could make use of. It is called Epernicus, and apparently was developed at Harvard University, just as a social and professional community. What differs is that it is tailored for scientists, providing for each person a sort of presentational web page with space for academic exams, list of publications and CVs. For me that helps a lot, because I have a safe space for my publication list on the web, and I do not need to carry it with me all the time, and others can quickly find it and contact me for a reprint (I have a lot of publications in the grey literature sphere). There are many occasions in life when a CV and publication list is requested, and only a few of these times are convenient in terms of searching for them.

Why not set up a personal web page somewhere and it will always be found by a search engine? Yes, sure, would be nice, but I am tired of web-authoring. Also, with the available online tools provided by Google (like this blog), Twitter, Facebook, Epernicus, etc., I am not bound to any particular computer. For some of these web resources I can use my mobile phone to update the web information. Well, with this blog, Epernicus CV, Twitter so my family can keep track of me, gmail, and the Google office suite, I feel I have moved away one more bit from the desktop computer prison, and into something more difficult to figure out how it works, and certainly at the heart of the grid. But this is only the beginning of how the web will become a much less physical resource over the next few years. If there are any ichthyologists out there, let’s meet at Epernicus. Maybe someone can inform me what the word epernicus means?

And, yes, I have read The Traveller and The Dark River. Find out what’s up in the Vast Machine.

From fishes to ZooBank

Fishes are among the most informatized organisms that I know. There may be a number of reasons for that, but reasons aside, the fact is that Daniel Pauly and Rainer Froese created FishBase independently of Bill Eschmeyer’s Catalog of Fishes, and ichthyologist Julian Humphries created the museum collection database with the collection management system MUSE back in the late 1980s, giving fish collections a head start in informatics. Since 1976 Joseph Nelson has published the Fishes of the World, now in its fourth edition, as an index to systematic ichthyology and with an eclectic classification.

Whereas FishBase has a given hit rate of 20 million per month and so is doing fine, the Catalog of Fishes is maybe less well known. It started first as a catalog of genera of fishes, but was expanded and eventually published as three huge volumes with scientific names of fishes, over 50 000, complete with type locality, current status, and literature reference. It is presently a web resource and updated frequently. For the layman it may look like just too boring, but for the scientists it is a goldmine saving enormously on the time of finding information about specific species and their names.

This kind of compilations is important, because biodiversity research is facing now an enormous problem with names. There may be 1.8 million named species, and many more million out there to be found, but only a million or so species have been secured in databases. And every year at least 16 000 new species are described.

GBIF have an initiative called the GNI (Global Names Index) to harvest all names, and a structure, the GNA (Global Names Architecture) to manage them. They will do this together with other acronyms such as PESI. In the meantime, the Catalogue of Life, a collaboration including the US ITIS and global consortium Species2000, have a checklist of the world’s species with just a little over 1 million in, and where FishBase is one of the best parts.

But we cannot have it like this, endlessly chasing names that people drop here and there in more or less obtainable publications. Zoological and Botanical nomenclature have to go modern and collaborate with information society. There have to be a registration system for names, and the habit of paper publication has to go away in favor of digital publication.

To those not familiar with nomenclature, the situation is the following: For a name to be available and thus accepted to use as a scientific name for a species, genus, or family, it has to be published on paper with a few more simple conditions such as a certain number of copies and a degree of obtainability. It is perfectly OK to publish 2 copies of a species description and give them away to 25 people who all except one throw their copy away within 24 hours. The single surviving copy is now the globally accepted token for the name of that species. Not surprising that many taxonomist spend most of their time searching for publications instead of doing real research.

Digital-only publishing is not permitted. Well, there is an exception for CD-ROMs with deposition in libraries, but it is a bit awkward and it may be difficult to find those CD-ROMs.

The International Commission on Zoological Nomenclature is the body that writes the rules for Zoological Nomenclature – of course with the needs and well-being of the taxonomic community taken good care of. The Commission is now seriously considering digital-only, what we call e-only publishing of zoological names; and seriously considering a registration system for old and new names.

Both proposals are controversial. Concerning e-only publising there is now a proposed amendment to the Code, and the Commission has invited comments and discussions. Some of the discussion is now published, and worth reading.

Formalisation of ZooBank as a registry for new names is maybe a bit further away, but unavoidable. In contrast to a Code amendment, it requires an infrastructure and running funds that are not immediately available. Nevertheless, Richard Pyle, ichthyologist at the Bernice P. Bishop Museum in Hawai’i, is working day and night to build up the structure for ZooBank. You can already get a glimpse of the future from the development site. There are already much more than 5 000 nomenclatural acts registered.

ZooBank will have a healthy starter boost from Catalog of Fishes, so from a fish perspective this is perhaps no big step forward. But notice, there is an ichthyologist programming ZooBank!

Yes, Ichthyology rules biodiversity informatics …

In the beginning …

This is a fast start blog to introduce myself (only a glimpse) and what possible kind of writings can be expected here.

As an ichthyologist, I will write mainly about fish. I manage two e-mail lists, my twitter, and blogs for two projects. Let’s see if there is more to say.

As a biodiversity informatician, I will try to connect fish with computers. I already post biodiversity informatics news on a Swedish language blog. Let’s see if there is more to say.

Naturally, I must first introduce you to those wonderful resources.

cichlid-l is the discussion list for professionals and others interested in cichlids. Cichlids are freshwater fishes found in Africa, South and Central America, Madagascar and parts of Asia. It is the second or third most speciose family of fishes (and vertebrates). This list is fairly old, started in January 1995.

eurofish-l is the discussion list for all other ichthyologists, but with an intended focus on Europe and particularly the activities of the European Ichthyological Society.

I will be back about the access to these lists, since they currently seem to have been locked up behind the firewall.

The FishBase Blog is the news blog in FishBase. FishBase contains information about all the world’s fishes, available for free on the web, e.g., on the Swedish FishBase server.

The Swedish Fishbase team also maintains its own news blog, in the Swedish language.

And finally, GBIF-Sweden serves news form the biodiversity informatics world in the form of a blog.

Ah, twitter, somewhat neglected: