Similar images

 Fish  Kommentarer inaktiverade för Similar images
Apr 302009

Has it not happened that you use Google search to search for images of say Danio rerio (a well-known fish). You get 16 900 hits. Unfortunately it is all too impossible to find a fish on many of those photos, because Google finds pages with the text Danio rerio having an image. And it takes time to browse through 16 900 images. This kind of image search is useful for finding the unexpected, such as anatomical drawings, phylogenetic trees, and people working on zebrafish, and definitely worth trying now and then. Without the image filter, you get 1 510 000 hits for Danio rerio, and that is just too much to browse in the hope of finding an image of the fish.

Google Labs now have a new tool under development that looks promising. It is called Similar Images, and uses some kind of image pattern recognition. What you do hear is that you specify a search for images as usual, e.g., Danio rerio, get the same result (but 16 500), but some images have the link ”similar images”. Click one of those, and you get a subset of the 16 500, and on succeeding searches using the same method, you get down to 300-500 look-alike images, and most likely you have exactly what you want within reach.

This might be a tool for matching photos of unidentified fish specimens, and could also be helpful to check fish identifications on the web. Maybe could be used for other things than fish? Seems to work well with Paris Hilton (a well-known human), but for what …?

Danio rerio from Wikimedia (c) Free use

Danio rerio from Wikipedia © Free use

Fish do not have fingers?

 Fish  Kommentarer inaktiverade för Fish do not have fingers?
Apr 272009

Although actinopterygian radiation seems to have made the most significant footprint in vertebrate diversity, with more than 30 000 Recent species, there are also scientists who looking into the origin of the less successful group, the sarcopterygians, among which the tetrapods are the terrestrial ones – except that some escaped back to the water (sirenians, seals, cetaceans, and the like).

Attending Catherine Boisvert’s defence of her dissertation The origin of tetrapod limbs and girdles: fossil and developmental evidence recently, I came to realize that the evolutionary quirk with tetrapods is not the possession of limbs – lots of actinopterygians have limbs, and many tetrapods lack them – but the presence of fingers. Catherine’s thesis is about the evolution of fingers and the pelvic girdle. The digits (fingers) sit at the end of the autopod (the hand and foot of tetrapods) and are homologous with the distal radials of the dermatotrichs (fin-rays) attached to fish proximal radials (the pectoral-fin base, homologous with the sarcopterygian/tetrapod limbs). Interestingly, the finrays and the digits form before the autopod and proximal radials in both sarcopterygians and actinopterygians. This was not well understood before, but Catherine and co-workers used fascinating evo-devo methods, catscan, recent lungfishes and salamanders, and fossils of early tetrapods to demonstrate this. Perhaps even more interesting, the front and hind limbs of tetrapods are remarkably similar, despite that the pelvic girdle of actinopterygians is a very tiny little plate of bone compared to the complex pectoral fin base. Catherine has advanced a theory about how the pelvic girdle developed into a support for the hind limb in tetrapods (making them four-legged). The real mystery, however, for me at least, is how come the hind foot is so similar to the front foot, and in particular, how come they both have five digits? Is this really the magic number? A handy come in pleiotropy?

Most fish that walk about use only one pair of limbs, either the pectoral fins, or, rarely (as in skates) the pelvic fins. It seems likely that early tetrapods were more like mudskippers than skates, but who knows.

My big question, which I never got to ask Catherine, is: what forced the fish up on land? I know the answer is out there somewhere, but I am always surprised at my prejudicial assumption that fish evolved into tetrapods. Or tetrapods evolved from fish. (Or aquatic animals have an intrinsic evolutionary tendency to become terrestrial). An obvious explanation would be that water was first, land later, and seemingly all fish ancestors were aquatic. It is still possible for a protist to have become terrestrial and evolved into a tetrapod without actinopterygian intervention (or they became insects?). So, the conclusion must be that those early fish that took on fingers were right away driven out of the water. Today’s terrestrial fishes, and our close relatives the lungfish, live in shallow water, swamps, and mangroves, in very particular habitats with strong seasonal or diel changes in water level. Maybe the mudskipper will take over the planet after us. It looks sympathetic anyway. Still has to do something about its hind limbs.

Image by Catherive Boisvert: Devonian landscape and fish actors making evolution.

Apr 242009

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?

 Ichthyology  Kommentarer inaktiverade för Where are the ichthyologists?
Apr 192009

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 […]

From fishes to ZooBank

 biodiversity informatics, Ichthyology  Kommentarer inaktiverade för From fishes to ZooBank
Apr 172009

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 […]

Sturgeon fever

 Fish  Kommentarer inaktiverade för Sturgeon fever
Apr 162009

A sturgeon (Acipenser oxyrinchus) once owned by King Adolf Fredrik, studied by Linnaeus,now housed in the Swedish Museum of Natural History collections.Photo A. Silfvergrip. Data . Image CC-BY. Once upon a time there was in the Baltic Sea a fish known as the sturgeon. Its existence in Swedish waters were known to Linnaeus and Artedi, […]

Fish from nowhere

 Danios, Fish  Kommentarer inaktiverade för Fish from nowhere
Apr 152009

Yesterday I mentioned briefly the leopard danio, a small golden fish full of dark spots, apparently a color mutation in the zebrafish Danio rerio, but described in 1963 as a species on its own with the name Brachydanio frankei. The leopard danio is a popular aquarium fish in its own right, which keeps its colors […]

Zebrafish in spirits

 Danios, Fish  Kommentarer inaktiverade för Zebrafish in spirits
Apr 142009

Zebrafish (Danio rerio) are probably the most important fish for understanding humans. They are small fish, 2-3 cm long and native to India, Bangladesh, and Pakistan. Most conspicuous about them is the contrasted coloration with alternating blue and white horizontal stripes, even extending onto the caudal fin. That means they are horizontal where zebras are […]

In the beginning …

 biodiversity informatics, Ichthyology  Kommentarer inaktiverade för In the beginning …
Apr 122009

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, […]

Kyplex Cloud Security Seal - Click for Verification