Taxonomy rules (nomenclature)

I was quite surprised to hear when many of our teachers and tutors gave feedback regarding the rules of taxonomic nomenclature (i.e. how to write the names of animal goups) – apparently, a significant few have difficulties with those norms. I recall having written a text going through the essential principles and the framework for how you write these formal names for my old website, which I shut down in favour of this blog. So, I thought I could post that text here as well, hoping it can clarify some confusion.

The taxonomic system for the hierarchical (ranked) classification of living organisms (and initially also of rocks, but that failed) is very simple. Organisms are assigned into different groups based on their characteristics, and these groups are hierarchical. The figure below shows the seven main types of groups. Kingdom is “higher” than phylum, while class is “lower”, and so on.

For some, but not all groups there are subdivisions of these group types, such as subclass (subdivision within a class), infraorder (subdivision within a suborder; i.e. infra- is “below” sub-), and grouping of groups – e.g. superorder (group of orders).

Since the system is hierarchical, organisms belonging to the same class also belong to the same phylum and kingdom. For instance, all animals belonging to the class Reptilia (reptiles, then) also belong to the phylum Chordata (animals with a notochord, or backbone) and the kingdom Animalia (animals).

Now, the order Primates (primates), although belonging to the class Mammalia instead of Reptilia, also belongs to the phylum Chordata and kingdom Animalia. This might complicate things, but it is simply due to that the two classes Reptilia and Mammalia both belong to the same phylum and (therefore) kingdom. 

Notice that the name of the class is written with a capital first letter when you refer to the actual group. If you instead write “carnivorans” (belonging to the mammalian order Carnivora; not equal to “carnivore”, which refers to a feeding strategy – not a taxonomic group), you are really referring to the members of the group, and you do not use capital letters. This rule is useful for distinguishing between, for example, Primates and primates.

While on the subject of formal rules, the genus and species are special. First, both are always written in italics. Always. Second, the genus name is written with capital first letter, but the species never has a capital. Third, you may refer to the genus alone, e.g. Tyrannosaurus, but never ever write only the species name. Never. This is because there may be several different species with the same name, (for instance, they may be named after the same discoverer) but they never belong to the same genus (if they do, they are simply not allowed to have the same species name). In this way, we get an endless variety of specific names for an endless variety of species. Finally, you may shorten the genus name to only the first letter (capital) followed by a dot and the species name (if you do not include the species name, you may not shorten the genus name ­– it would be silly to write something like “T. had remarkably short arms”). For example, we take the genus Tyrannosaurus (species name is excluded, since I refer to the genus), which has one species: Tyrannosaurus rex – although some researchers argue that Tarbosaurus bataar really belongs to Tyrannosaurus; in that case, we would also have Tyrannosaurus bataar  (the species name is the same, but is assigned to a different genus). Notice that I should not shorten the genus name here, since it may be unclear what I mean by T. bataar.

Names can be discarded or invalidated, usually by showing that two very similar species actually are the same, in which case the name given first is the one that remains valid. Rejected names are written within quotation marks, and never italicised. A classical example is that "Brontosaurus exelsus" and Apatosaurus ajax were shown to be the same species (and therefore also belonged to one and the same genus); Apatosaurus, being the first to have been described and named, was kept (both genus and species name).

Another notable convention is that families tend to end with -idae, superfamilies with -oidea and subfamilies with -inae (their members would then be -ids, -oids, and -ines, respectively). For example, we have the Hadrosauroidea (superfamily), Hadrosauridae (family) and Hadrosaurinae (subfamily).

Nowadays, the taxonomic system has been overshadowed by phylogenetic systematics, or cladistics. Cladistics is favoured because it systematically investigates evolutionary relationships, rather than just putting the organisms into different groups; cladistics tries to work out how they evolved, and how closely related different organisms are. Taxonomy, on the other hand, merely groups similar-looking organisms together in order to make some sense of the overwhelming chaos of life we have out there.

The groupings can differ quite a lot between taxonomy and cladistics, since cladistics has a predilection for groups that include all the descendants within an evolutionary line (i.e. monophyletic clades). Therefore, cladistics disregards the group Reptilia, as it does not include birds (class Aves) and mammals, both which have their origins in the reptilian evolutionary line. Instead, cladistics just group them all together as Amniota.

Bristol Aquarium

This Sunday, I visited the Bristol Aquarium with a couple of friends from school. I had never been to an aquarium before, so it was quite an experience!

It was frustratingly difficult to take even decent photos through the glass tanks of the fish that just wouldn’t stay still. Consequently, most pictures were something like this:

Of course, I will only show the least blurry photos in this post. For that reason, the post will also be quite short – for better or for worse.

Among the animals that were easy to photograph was the colossal lobster that seemed too large to be bothered to even move. You can see the camera casing I placed outside the tank as a scale.

As my friend Joe pointed out to me: note that the lobster has two different claw types, probably adapted for different forms of food manipulation – the more robust one may be for crunching hard shells, and the more slender claw could have a flesh-cutting function.

Fluorescent invertebrates made rather spectacular sights. Here is a medusa (medusozoans) called Aurelia (looked it up on Wikipedia).

 

And here are some sea anemones (anthozoans):

Both are cnidarians, invertebrates with a radial symmetry (which more or less means that they are symmetrical along various different planes round the centre of the organism); most have tentacles with sting cells (called cnidocytes; hence the name) that are used to capture prey. The group also includes corals, within the subgroup Anthozoa – so they are put together with the sea anemones. If memory serves, the characteristics that define the group has to do with their reproductive cycle, but I have not looked much into it yet…

Corals there were plenty of in the coral reef tank.

Dragons, hippogriffs and other mythical creatures – if they were real, what would they be?

Among my fantastic friends here in Bristol, there is one particularly peculiar: Shirin [shirine]. Apart from being generally wonderful, she is also weird in many ways, so a blog post on a few of her ideas is a must.

She is completely obsessed with dragons, having collected hundreds of models, trinkets and whatnot throughout the years. Since we are both paleontology students, naturally, we discussed the potential phylogenetic position the dragon lineage would occupy in the tree of life, were they real. I had recently been thinking about that, and was leaning toward them being an offshoot of the Rauisuchia – an extinct group of land-living relatives of modern crocodiles, though much larger. Like dinosaurs, birds and mammals, the rauisuchians had an erect limb posture – a feature also depicted in many dragons, and characteristic of highly active predators or grazers. I will not dwell into details here, but an erect limb posture is associated with a more efficient respiratory (breathing) system, which enables the animal to use energy more efficiently to sustain a high-rate metabolism, something that likely is needed for a creature capable of breathing fire. In other words, the similar limb postures, and the sense this similarity makes in terms of  its associated function, hints toward a connection between dragons and rauisuchians.

An artist’s impression of the rauisuchian Postosuchus. Image from http://www.bbc.co.uk/nature/life/Postosuchus

Now, do not forget that there are other animals with an erect limb posture. However, there are other morphological similarities that make the Rauisuchia a good candidate for the ancestors of dragons. Most dragons have scaly skin, which rules out a mammalian origin, though not the therapsids (advanced members of the Synapsida, more colloquially called mammal-like reptiles, since they are a sort of transition group between reptiles and mammals), which also had an erect limb posture, though no fur. The skull morphology of most dragons is very reminiscent of that of modern crocodiles, with the anteriorly flattened snout and anteriolateral nostrils. In addition, dragons are often depicted with conical teeth, just like those of modern crocodiles.

Left: an artist’s impression of a dragon; right: a modern crocodile. Notice the similarities in snout morphlology. Pictures from – left: http://www.chrisscalf.com/Sci%20Fi%20Portfolio/SciFi%20Html/Dragon%20Fire.html ;
 right: http://ozmagic.homestead.com/australiancrocodileaborigine.html

That skull form is close to that of rauisuchians, although their skulls are deeper and flatter, but also similar to that of some carnivorous therapsids, in particular the gorgonopsids.

Left: a model of the head of the rauisuchian Postosuchus; right: a gorgonopsid therapsid, a creature not far from the first true mammals, and another possible precursor or dragons, based on superficial skull similarities. Pictures from – left: http://www.cmstudio.com/postosuchus.html ; right: http://wonjae.files.wordpress.com/2010/05/gorgonopsid_2.jpg

However, Shirin made a good point: some dragons are depicted with feathers, which has only been found in the dinosaur lineage. The rauisuchians diverged from the dinosaur ancestral lineage at the very base of the archosaur group, which unifies dinosaurs, pterosaurs and crocodylians, around the early Triassic period, about 20 million years before the dinosaurs first appeared; the therapsids are separated from the dinosaurs by around 100 million years of evolution. Feathers are thus unlikely to be found in descendants of either of these groups, since the relation to the feathered dinosaurs is remote.

Dragons must then have come from dinosaurs, Shirin argued. The reason why I was doubtful about that is because of the quadrupedal stance of dragons – dragons are definitely carnivorous, or perhaps omnivorous, but the only four-legged dinosaurs were (more or less strictly) herbivores – no one was adapted for a meat-based diet. Dragons ought to have emerged from the theoropod group, if from any. When I later thought about it, the idea makes sense in many ways: the Theropoda is where most known feathered dinosaurs belong to; they had highly pneumatised bones – hollowed-out with air holes – making them very light-weighted, something important for flight; it gave rise to flight at one definite point, so it had the potential for possibly generating another. However, the theropods are strictly bipedal, and show no signs of reversal to the (not directly) ancestral quadrupedal posture.

After some more thinking, I thought of the spinosaurid family, a rather odd type of theropods with crocodile-like snouts bearing conical teeth and rather long, powerful arms. The snout and tooth shapes drew my mind to dragons, and the well-developed forelimbs could be a start to developing a four-legged stance. What characterises at least Spinosaurus is the long sail on its back, supported by greatly elongated upward projections from the dorsal (back) vertebrae. Could the development of this membrane between roughly parallel bone outgrowths be the forerunner of the flight membrane on the dragon wings? Could those long vertebral processes have been to anchor strong back muscles used for flight? It may seem vague, but there might be a connection here.

Leaving the dragon riddle unresolved for now, let us turn to another one of our discussions: Shirin’s hypothesis that hippogriffs – majestic beasts with the hind part of the body (trunk, tail and hindlimbs) being of a horse and the front, covered in feathers, resembling an eagle’s – are close relatives of the platypus, a modern member of a primitive mammalian group – Monotremata – which has fur, but a duck’s bill and lays eggs. Half of the platypus is a mammal, and half is a bird; the same goes for the hippogriff.

An interesting observation, but the respective mammals and birds they are a chimera of are not closely linked at all. Ducks and eagles are possibly remotely related – I’m not sure of bird evolution, but it is not an unreasonable assumption that they are only distantly related – and the mammalian part of the platypus – a large, elongated trunk with short, stubby limbs sticking out from the side of the body and with webbed feet – is not reminiscent of any other mammal I have ever seen, and certainly not to a horse. If the hippogriff and platypus are sister taxa, one would expect at least some similarity in the animal groups their respective body parts mimic.

Left: the platypus; right: an artist’s impression of the hippogriff. Images from – left: http://troghead.blogspot.co.uk/2012/04/platypus.html# ; right: http://hogwartsrpg.wikia.com/wiki/File:Hippogriff_drawing.jpg

Still, Shirin’s important observation deserves an explanation, and it can be found in convergent evolution – when unrelated organisms develop similar traits as a result of adapting to similar conditions. The main problem with this idea is that the platypus is amphibious (living both in water and on land), while the hippogriff flies: they have adapted to two completely different media – water and air, respectively. An analogy to how improper an argument of convergent evolution between the platypus and the hipogriff can be found in comparing the fish fins with bird wings.

These are the kind of things that go through our heads…

Admit that it is awesome! Hahaha

Coming soon... I think...

Right... so the workload of the courses is starting to become more and more evident, so there will probably be little time for major blog posts in the near future. I might occasionally throw in some text about a topic I find particularily fascinating and important enough to share here, but that would be sporadically only.

However, I have been completely entranced by the early evolution of land plants, so I might make a decent post on it in the near future. I live right next to the botanic garden, which has a display of the evolution of plants using extant (non-extinct) species to represent the main groups at different time periods. I went there on a sunny (!) day and took a bunch of photos; next, I will learn as much as my actual, curricular workload permits, and then use those as illustrations. I hope that will turn out good.

The first days in Bristol

Soon a week ago, on Friday the 28^th of September, I arrived late in the night with my parents at a hotel near Temple Meads, one of the main train stations in Bristol. The journey from Sweden had been alternately stressful – hurrying to make sure we were on time for everything – and calm – during which I was growing increasingly nervous about this big move, this new life that awaited on the other end of the trip.

Up until some weeks earlier, moving to Bristol had been so far away in the future that I did not think much about what it would be like. I was accepted on the programme Paleontology & Evolution (MSci) [the British spell paleontology with an additional “a” before the “e”, one of the few British spellings I just cannot stomach] sometime in March, and as information and instructions for pre-arrival preparations were sent to me, I processed it all a bit at a time, but sort of absent-mindedly: it still felt like some kind of dream– at any time, some problem could surely arise that would ruin everything and prevent me from going – or maybe it was all a practical joke thrown on me by fate.

As the date of moving came closer, however, I realised that this actually was going to happen. When I started packing for the move, it was definite: my life would start over. Yikes.

After that realisation, my stomach made a few somersaults here and there. But, my nervousness was nothing in comparison to my mom’s, whose little boy was leaving her after all these years.

After an internally tumultuous journey, we arrived just in time to get a late meal at the hotel before taking a shower and preparing my bag for the excursion to Somerset Coast.

The thing about the excursion is that the others met in Bristol and departed together around mid-afternoon on the Friday, which was problematic for me as I arrived around 9.30 pm. However, I had planned this out together with the excursion leaders beforehand, and would go to the excursion site myself on Saturday morning. I was to take a train from Bristol Temple Meads to Bridgwater, wherefrom I would ride a bus to Watchet, where I would meet the others.

I made plenty of mistakes in the morning, though. I had been told that breakfast was served at 6.30 am; the train departed from the station (about five minutes away) at 7.18. Thus, if I ate quickly, I could make it to buy the ticket and get on the train. However, I made the false presumption that my phone alarm would adjust to the time zone change automatically (England is one hour behind Sweden)… which it did not. When I came down to the lobby at 5.15, having slept less than four hours, I was told that breakfast was one and a half hour away: breakfast begins at 7.00 am on weekends.

Well… there was not much to do… I knew I would not manage to go back to sleep, so I sat on my room, watching the morning news.

It all sorted out eventually. I made it to the train in good time (dad had gone to the station to buy the ticker while I had my breakfast – a brilliant idea that would not have had crossed my mind at that point). However, here came the next problem: they did not call out the names of the next stop in the speakers, so I had to be alert all the time – on a journey of more than an hour, having had only a few hours of sleep last night – and read the signs at the platforms.

None of this had been foreseen, which is why it made such a mess for me. However, I had looked up the way to the Bridgewater bus station from the train platform very carefully before leaving home, and that trip went perfectly well, despite my inherent talent for getting lost.

When I joined the rest of the excursion group, I was shocked by meeting some good seventy students; I had imagined we would be between ten and twenty only. I was greeted with many strange looks – of course, they had got to know each other the night before and already formed small groups. It would be trickier to get to know people than I had expected. I just don’t function socially in such large groups – naturally, I did not dare approach anyone yet. 

Update coming soon

I am currently mid-way through Fresher's Week – the first week for new undergrauates at univeristy ("freshers"), which is basically a week without teaching, dedicated to sort out formal matters such as registration, instructions and information about the course, content, assesment, life at the university, social life, societies, etc. etc. It is a fantastic way to get your uni life started before it is submerged in heavy studies.

I have truly had an epic time, and I will write a post on it (including the journey from Uppsala to Bristol and pre-sessional field trip to Somerset Coast, which was special for us new students as the Department of Earth Sciences, and gave us a head start on making friends!), updating you about how I am doing right now, and how drastically my life has changed (for the better, I think!). I will try to have it done by the end of Fresher's Week, so that I can focus on the lectures on Monday.

(If you were misled by the title of this post, raise your hand. If you resented being misled, please do not bother...)

The best iPhone app

I just found what must be the most amazingly genious free iPhone app: Taking Pictures With Dinos!!

With it, you can add a dinosaur to pictures you take with your ordinary phone camera (I don't think it works on pictures you already have taken, though)!

Just to try it out, I took a shot at my laptop, which now has a T. rex on top of it :)

 The free version comes with four dinosaurs: Tyrannosaurus, Diceratops, Argentinosaurus and Suchomimus. You can get additional collections of dinosaurs (dromaeosaurids, ceratopsids, sauropods, theropods, and segosaurids) for about $1, I think. Given the infinite possibilites this app gives for any nerd, it shure is worth it!!

Boy, am I going to have fun with this at the airport tomorrow! (I'm leaving for Bristol then!!!!!)