To me – to you: directions and descriptions

Having covered the ongoing saga (though to be honest it’s less of a saga than a small novella) of the ‘cranial-caudal’ descriptions issue, it seemed an appropriate time to bring up the ideas of directions in anatomical descriptions. As I noted in the earlier post, the point about directions in anatomy are to be clear and concise and to provide an unambiguous definition of something to avoid confusion for the readers and researchers who want to follow what you have written accurately.

It should be easy to see how people can get confused without being careful about terms. You could describe a feature on a humerus say as being on the same side as the thumb, but rotate your wrist and suddenly that point of reference disappears. Most people would describe their chest as facing forwards, but in a quadruped that same structure (the ribcage) would be facing down towards the ground, and while the metatrsals in our feet face flat down on the ground in most other animals they would face backwards. If you used terms like this it would be easy to get lost or end up comparing the wrong things hence the general standardisation of terms. I say general of course as there are still issues here and there that crop up, like the cranial-caudal one, or those of the scapula.

So here as a brief guide / aid memoire, are a few of the basic directions used in anatomical descriptions for the orientation and position of bones and their features. Please excuse the very basic outline drawing, it was the best I could do* quickly:

Anterior (or cranial) – towards the head end of the animal.
Posterior (or caudal) – towards the tail end of the animal.

Dorsal – towards the back.
Ventral – towards the front.

Medial – towards the midline (something can also lie medially like vertebrae).
Lateral – away from the midline.

Proximal – towards the body.
Distal – away from the body and towards an extremity (so you can also talk about the distal tail for example).

Palmar (or plantar)> – towards the palm of the hand / sole of the foot.
Dorsal – towards the back of the hand / top of the foot.

Labial – towards the lips or outer part of the mouth.
Lingual – towards the tongue or inner part of the mouth.

These rather obviously all come in pairs of opposites but they can be used together or in combinations. So your spine is medially positioned and runs anterio-posteriorly (from front to back) and while your orbits face anteriorly (or rostrally if you prefer) you can swivel your eyes to face dorso-laterally (up and to the side) or medio-ventrally (down towards the middle) if you so choose.

The point is, and should be, that even as joints move and rotate and even whole body plans change and evolve (humans stand rather differently to monkeys, let alone cats or mice) the points remain relevant and accurate and directly comparable. Thus providing a secure set of references to make both descriptions and comparisons accurate.

*and by ‘do’ I mean ‘bother with’, but for this it should be more than sufficient.

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Cranial-Caudal vs Anterior-Posterior

This is something I have been avoiding for a while as I know for a fact that this is divisive in the dinosaur / archosaur community and incidentally I’m probably on the minority side. However, regardless of the divide, it is important to know that the division in there and why.

Although I have not really covered the issue of directions in detail before, the central idea that scientific writing should be clear and concise is something I have expounded on before. In short, when describing bones (or teeth, positions, rotations about joints etc.) anatomists use a series of words to accurately describe directions to make things clear and concise. Obviously terms like up, down, left, back, rear and so on can vary depending on your point of view or if something can rotate (you can hold you palm facing up or down for example) so having a set of directions based around the skeleton itself eliminates much of the confusion.

However since palaeontology and anatomy as subjects evolved well before phylogenetics, initially different groups of animals ended up with different shorthands to reflect the different people working on them and the different issues at hand. Thus while reptile (and dinosaur) researchers largely used anterior and posterior to denote a direction towards the front or rear, most bird workers used cranial and caudal (literally towards the head and towards the tail) to mean essentially the same thing. Of course once it became clear that birds were dinosaurs, many dinosaur researchers started to use cranial and caudal as opposed to anterior and posterior (the situation is of course more complex than this, but that’s my take on it in as few words as possible).

The consensus seems to be moving towards this as the right thing to do but I have to say I disagree. I think the clarity issue is at stake with these terms for two slightly different but related reasons:

1. Frankly I think the terms can sound silly when in use the beak or rostrum of a skull is anterior (i.e. in front of) the orbit (eye socket). Under the ‘avian’ system you would say that the rostrum is cranial to the orbit, but both of them are in the head itself, so essentially something is in the head direction of the head relative to something else in the head. Sure you know what it means, but I don’t think it is as clear as it can be and it is almost oxymoronic.*

2. Similarly but even worse, we have the problem with vertebrae. Vertebrae in reptiles are typically divided into cervical (neck), dorsal (back), sacral (in the pelvis) and caudal (tail) vertebrae – you may therefore have already spotted the issue. If you want to talk about posterior dorsal vertebrae these are caudal dorsals, and posterior caudals are caudal caudals. How can this possibly be considered clear? You actively have to stick the word caudal into positional details of vertebrae that abut the caudals or relate to the caudals but are not caudals? You can end up saying that the caudal dorsal vertebrae resemble the cranial caudal vertebrae but not the caudal caudal vertebrae or the caudal cervical vertebrae. Oh good.

That’s it really. In short cranial = to the front and caudal = to the rear. These terms are common and indeed are increasingly so, but I often find them awkward and as such I don’t think they serve the community as well as they could. Perhaps I’m just slow, but I really often do have to re-read phrases about ‘caudal cervical vertebrae’ to remember that we are dealing with the neck and not the tail and it seems so unnecessarily complex. I suspect at least a couple of readers will try to correct me in my thinking and I’m willing to be persuaded, but I’ve yet to hear a convincing argument as to why ‘cranial-caudal’ is better than ‘anterior-posterior’.

*Note: here ‘rostral’ meaning ‘towards the snout’ can also come into ply in place of ‘cranial’ though of course this still does not help when you want to say that the rostrum is rotrally positioned (OK, that’s obvious, but the point is valid), and of course a horn say that extends in front of the rostrum becomes very hard to describe!

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Some specimens are more equal than others

I got into a discussion with my colleagues the other day about the merits of collecting multiple specimens of taxa versus collecting something new. The reality of course is that there is rarely a choice to be made – you bring back everything you find in the field that you can. However, as a hypothetical discussion it is interesting since of course you can do very different science with 10 specimens representing 10 different species and 10 specimens of a single species.

This debate aside (one for another time) it led me to get around to writing this post which I have long intended to complete on the differing importance of different specimens. It is understandable that some people might think “so you have 25 Triceratops, so what? Surely once you have one good, complete one, there’s not much more to learn?” but of course this is far from the truth.

As I have covered before on my series of posts on taxonomy, multiple specimens can give you a huge insight into the variation of fossil animals as living organisms – be it intraspecific or sexual. If animals are of different ages then you can learn about ontogeny and growth and of course there is always the change that a new specimen shows off some odd characteristic like a pathology, bite marks from a predator or something like this.

Some specimens (and the fighting dinosaurs are a great example) cannot easily be prepared for research, no matter how good they are (or in this case, not without losing a lot of other important information). Another specimen where all the bones can be separated out and viewed and analysed in 3D is great therefore allowing all kinds of extra information to be accessed and things like range of motion in joints to be examined firsthand. Similarly, having a ‘sacrificial’ specimen is great – no one wants to chop up a brilliant holotype to look at the bone histology or look at replacement teeth or the braincase, but a second specimen allows you to be a bit free-er with your methods and destructive sampling becomes a serious option – even a very fragmentary partial bone can be enough for this.

OK, maybe we don't need to collect this.

So while obviously for most palaeontologists a single complete skeleton is a great find, every little specimen is valuable. However, it would be a mistake to consider each of equal value – a single broken femur is good for destructive sampling, but an articulated leg is more useful and obviously several complete animals are better still. Even this varies from researcher to researcher – histologists are likely overjoyed by a bunch of otherwise largely unimportant partial specimens that they can sample while behaviourists won’t get too worked up until they hit a whole herd preserved together.

I imagine most of this is largely very obvious, but still there is typically always one more angle to think about and I hope I may have highlighted one or two here. It’s easy to get stuck in the mindset of ‘what would I do with that fossil’ which might be very useful for you, but not always that of your colleagues.

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A bit more on convergence

Before my brief hiatus with a trip to Shandong (very worthwhile, despite the illness that stuck me down) I was talking about convergent characters and the importance of examining all the available evidence and not just a select feature or two. However, that post was written rather quickly and I didn’t have time to expand on it in the way I wished so now I’ll push on with a few more observations.

While last time I mentioned only specific characters like spines or claws that can arise convergently, it is course possible for entire suites of characters to evolve convergently. While a big and specialised ungual will help you break into a termite or ant nest, a well evolved termite eating animal will have modified arms to provide power to that claw, and have a long snout and / or tongue to reach those termites, perhaps specialised sticky saliva, digestion suited to large amounts of formic acid, lost teeth and more. Eating ant is more than just a claw, so animals that specialise for eating ant are likely to have whole sets of characters which all help to increase ant-eating abilities and thus evolve in the same way in multiple lineages – in other words convergence. After all, if you want to run fast, having a long lower leg is great, but having a long metatarsal too, and cutting down on the number of toes, and actually shortening the femur as well are even better.

This takes us nicely to the second point – that when those suites of characters combine in certain parts of the body this can cause taxonomic and systematic problems. Animals that are highly specialised for running often have the characteristics I note above, but what if you recover a fossil that is *just* a pair of legs? If you have an anteater arm then you will spot the big claw and modified ulna, but there are also some other features that should help reveal its true identity – pick up a maniraptoran theropod leg though and things get trickier. It is perhaps no surprise that there were early questions over the phylogenetic position of things like alvarezsaurs and oviraptorosaurs with their specialised cursorial legs – there is quite a lot of convergence there.

Finally, we come to a point about defining characteristics. Things can look very different from a general description or a very detailed one and apparent convergences can vanish in a puff of adjectives (like the flippers of penguins and turtles shown here). Both birds and pterosaurs have wings, but one has feathers and reduced fingers, the other a hugely elongate arm and membraneous wings. Bats can try and muscle birds out the way with their long wingers and ‘skin’-like wings, but again, closer examination shows that pterosaurs rely on a single finger to support their wing, not a whole hands worth. These are, of course, especially coarse examples, but I hope the point gets home.

That largely wraps up convergence, or at least as much as I wanted to say about it for now. Coming up soon, something else. For once I’m a bit bereft of pre-prepared posts so I’m not sure what I’ll get round to finishing up and posting. Stay tuned!

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Spiny-ness in mammals and rampant convergence

As the title has already given away, I’m going to talk about mammals a bit on here for once (well, OK, they have cropped up occasionally before) but as a set-up to a point about convergence and evaluating evidence so it will hopefully be instructive and not overly extant mammal-y for those who like their extinct archosaurs. So onto, as also already given away by the title, spines in mammals.

Proof by illustration

One might think that after developing as a science for the last two hundred years, palaeontology would demand some pretty rigorous proof of a concept before it enters the area of ideas that one could consider ‘general consensus’ or perhaps nowadays more accurately (though less inclusively) ‘passed peer review’. However there is still one holdover from the early days that crops up from time to time in the literature (though far more often in general ramblings of unpublished ideas and online discussions) that being the concept that an idea is convincing if you can produce some nice looking artwork to demonstrate it. Essentially, proof by illustration.

Tremble ye mighty referees and authors

Possibly. Anyway, I’ve now been formally taken on as one of the associate editors of the palaeontological journal ‘Historical Biology’ (my thanks to Gareth Dyke for his invitation to join the board). Having preached much about peer review, reviewing and writing papers and even the editorial process I hope that I can put this all into practice. This might put more people off than it encourages, but those of you writing palaeontological papers, (perhaps as part of the PPC?) an at least consider HB as your target journal.

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Memory and the fossil record – laboured analogy time

It occurred to me the other evening that the human memory can serve as quite a good analogy for the fossil record. While I have before covered some of the issues of bias in the fossil record, this might serve as something a little easier to think about since it’s based on something we all experience. Anyway, I’ll launch in and see how far I get before the whole edifice breaks down…

Keeping up with the literature

My colleagues Mike Taylor and Andy Farke among others have done an admirable job of promoting the concept of open access in palaeontology, both for data and for the actual research papers that academics produce. However, while this is on the whole a very good thing, it has I believe (in conjunction with other phenomena) produced problems from the frontline scientists whom it is supposed to help.

While what I am about to write may be seen as a complaint it should not be – it is an observation. It is for me currently problematic, but that does not mean that I do not support open access (I do) or that this is a huge issue (it isn’t) or that on balance open access is a bad thing (not true either). With change comes problems, some foreseen and others not, and most if not all ultimately overcome or sidestepped to the general satisfaction of most so this is not something I expect to be a long-term issue. Here I simply want to illustrate a couple of problems that I have not seen commented on or discussed before. So with this in mind, what’s the problem?

Casts vs sculptures

A long time ago in the dim and distant past on here I wrote about fossil chimeras and mounting skeletons and have since written about fake fossils of various kinds. In these I rather breezed over some of the different ways that fossils can be produced for display and it seems worth going over in a little greater detail and roughly defining a few terms to make things easier for people to understand and distinguish between the various things out there.

Increasingly, genuine fossils of large animals are not on display in museums. These are expensive and valuable artefacts and scientists need to access them, and the museums need to protect them. Big dinosaur mounts that tower into the air made up of original fossils that are hundreds of millions of years old are therefore rare. They are hard to examine, and difficult to keep clean and if they ever fell over…. However, even the most complete of big dinosaur mounts are often not as they seem and can be completed using a number of different techniques.

Here then are the ways that you can complete your dinosaur fossil:

1. Original material. While these are becoming rarer, there are a significant number of mounted skeletons being produced composed mostly or entirely of original fossil material. Since there are pretty much no *totally* complete dinosaur skeletons in 3-D, the odd part of another specimen may be used to fill in the gaps, effectively creating a chimera.

2. Repaired material. Even if you do have a complete specimen, the odds are there are a few chunks missing – a humerus with the end gone, teeth lost from the jaws, or the neural spines broken from a few vertebrae. These can still be used with the missing parts repaired and completed from plaster or a similar material.

3. Casts. You can of curse simply make a direct physical copy of the bones of your specimen and mount them, or from another specimen to fill in the gaps and these are casts. Most big specimens nowadays are casts of real specimens supplemented by sculptures of missing bits.

4. Sculptures. Finally, you can simply model the missing pieces from scratch and make them to fit the gaps and what you know of the existing anatomy or from close relatives. Sculptured bones run the full length from inept plasticine-like creations that look only vaguely like bones right through to superb ones that can even look better (since they have no breaks or distortions) than the originals.

A selection of casts and sculptures of dinosaur claws and various teeth.

Telling these different ‘bones’ apart is not normally too difficult with a little practice (though across a darkened dinosaur hall it’s not always easy). Typically original material looks organic in a way that even casts do not – natural swells and breaks and just the texture of the bones will look ‘right’. Repairs to original material are often crude, but in any case the instant change in texture and colour between a sculpted piece of plaster and the bone itself should be clear. Sculptures (whether as repairs or as whole replacement bones) often have little texture on their surface beyond a few scratches or dimples and are often a give away as their surface is so smooth. Finally casts often loose a little of the detailed surface texture of the originals from which they are copied but can usually be distinguished by their colours. Real bones generally have a range of colours (if minor) to them when casts are typically made using coloured resin or are pained after production and so are a uniform colour.

That’s quite probably more than enough of casts and sculptures, but this should serve as a guide to what is, and is not, real in museums and how to tell them apart and why this can be important.

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The casqued cassowary

While we are talking birds with odd beaks, skulls, ornaments and all that, it seemed most pertinent that I dig up this image of a cassowary from my collection. The crest at the top of the head is more properly called a casque and while studies show that it certain does have an ornamental / signaling  function, it is used for a few other things as well including clearing foliage and detritus off the rainforest floor where the animals live.

To return then to yesterdays general theme, it is usually a bad idea to go looking for extra possible odd functions and features in fossil animals. If you have a good set of data that strongly supports a given function of a morphological feature – don’t try and then second guess yourself with a  raft of extra odd (and untestable) features just because they crop up in one or two extant organisms.

Case in point being this one, I suppose it’s possible something like Monolophosaurus did use it’s crest in a similar way to a cassowary, but I wouldn’t want to argue that and nor is it common enough or tied to an obvious structural feature that you could realistically test it on the dinosaur.

However, when trying to work out the possible range of behaviours that an animal may have exhibited or when faced with something unusual, it can be well worth digging around (so to speak) in the literature on extant animals. There is such a raft of unusual things that living animals do and features they have that it would be impossible to consider them all when looking at a new fossil – to do so would be a waste of time and effort and a great many simply could not be assessed properly. They can provide a source of ideas and information that could easily be missed otherwise so as ever a balance must be struck, but stick to those that can reasonably be tested and avoid the extreme.

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Underprinting and more tricky tracks

A recent discovery of ‘giant’ sauropod tracks in France has got the media all of a flutter and it seemed a pertinent opportunity to return to the concept of ‘tricky tracks‘ and the misinterpretation of fossil footprints. The media are especially impressed that some of these impressions are nearly 2 m across and while I have not seen anyone *directly* claim that these match the feet that left them (and nor have I looked that hard), I rather imagine most people will jump (not at all surprisingly) to that conclusion. But is this really the case? Are there sauropods out there with a pes six feet across?

Well once again that rhetorical question at the end of the first paragraph has a pretty obvious answer – no, not really. While I have not seen any researchers quoted on the French tracks or indeed seen any decent close-ups, I find it hard to credit that there were sauropods with feet this big, since frankly they would have trouble getting their feet past each other when the walked, and scaling up from the bones of sauropod feet an animal leaving tracks that big would be getting on for a size that is hard to comprehend. Hundreds, even thousands of tons I imagine – in other words, beyond credible. So what’s going on here?

One explanation is that the tracks as preserved are showing the effects of the substrate they were made in. In short, a heavy animal walking across very soft mud will gunge and slop the stuff everywhere and will leave a wide area affected by its passing at each point that a foot hits the substrate. In other words, big feet and soft mud can make for even bigger tracks.

However I suspect the answer is another related but somewhat different artefact – underprinting. Imagine a nice heavy sauropod putting its foot down on some relatively soft, but still firm, sediment that lies in multiple layers (like lots of mud layers that have built up on a tidal flat over a few weeks for example). Now the actual print the animal leaves on the surface of the mud will likely be quite clear and deep, and will indeed match the foot that left it. But as we move down through the layers the force will dissipate and spread out. On the second layer the impression will be less deep, less clear and, crucially, rather bigger. Go down a few more layers experiencing the same effect and what you are left with might well be recognisable as a sauropod footprint, but this undertrack might also be several times bigger and not very distinct. You might well have a 2 m wide sauropod track, but not a 2 m sauropod foot. An incredibly important, and hardly subtle distinction, but one rarely, if ever, discussed in the media or even some palaeontology textbooks.