So … hi there. How have things been with you? I’ve been away from this blog for a while, but don’t worry!: I haven’t been idle … not all of the time anyway.
Much of my time over the past 18 months or so has been focused on one single piece of work. This hasn’t been the only thing: I’ve appeared in a couple of talks on phylogeny at SVPCA and Progressive Palaeontology, and by ‘appeared in’ I mean ‘presented’. (I’ve recently updated my Academia.edu page with the details of these.) Aside from those, my mind has been fixed on the taxonomy, I’ve written an overview as one of my early blog posts. This has now come together to form a monster of a manuscript that I’ve just submitted.
However, the fruits of that work aren’t what I’ll be talking about today. By ‘monster of a manuscript’, I mean some 250 pages of body text, plus many for references, captions, and index: 364 pages in total, and add on the figures and plates themselves too. (Note the Oxford comma there, which I have a new-found fondness for. Yes Mike, I realise that this is hypocritical considering the argument about it that we had last time we met.) This post, therefore, is about how I wrote this, and how I put it all together, or, more specifically, the computer programs that I used to do this. It, this post, may be a bit of a curiosity, but it’s a curiosity that I shall indulge myself in, much like my eventual post on typography (stay tuned!).
For those who can’t wait, or, potentially rightly, expect me to not write about this for a long time, you can find many interesting things on the Web. A few of my favourite places to look are Typographica, Typophile, and, of course, there is Wikipedia. Another interesting point is that I wrote this blog post using the type family Linux Libertine. Intended to be a superior replacement for Times New Roman, it succeeds at this very well. It is also free, includes glyphs for both Greek and Cyrillic, which I have used, and comes with compatible serifed (Linux Libertine) and sans-serifed (Linux Biolinum), display, and monospaced fonts.
Getting the words down
The first challenge is, of course, getting the words down. This assumes that you know what you’re writing about, and have the ability to do so: while this is typical for academic writings, it may not be the case in writing fiction novels, for example. This, in itself, is a very large can of worms, which I may address some day. Suffice to say: if you are doing a PhD, you’ve probably got this at least somewhat sorted.
My work consisted of lengthy descriptions of several ichthyosaur taxa: going through each bone: describing its shape, what it joins to, and what’s around it. This is simple enough when you have the whole bone in front of you, but less so when it’s only a bit of it, and you’re having to compare it to a photo of another fragment that’s housed in a different museum.
However, that’s not where I’m taking this.
I dislike Microsoft Word. It works, yes (mostly; ooh! that’s a snide comment right there), but I find it difficult, and it does not work well with the way that I work. Doubtless there are many things I could do to improve my relationship with it; I’ve tried. I prefer Apple Pages as a word processor, but that is quite a bit more limited in extended functions. This is especially true for the most recent version. Maybe more features will be added?, but I’m not sure when or how well. Pages could be great: I found it highly useful for doing my undergraduate reports, essays, and dissertation. It has lost some of its sparkle since then. They both suffer, as I’ve realised since starting to write lengthy, bitty pieces, from being too linear: they excel at starting at the beginning, going towards the end.
Let me clarify. When writing lengthy descriptions, particularly when each section is on a specific bone, I found it helpful, and easier to write by jumping around: a bit here, a bit there, compare that with this, and so on. This was easily accomplished in the software that I used: Scrivener for Mac.
Scrivener is a series of programs by Literature and Latte, available for Mac, and Windows, with an iOS version in development. It is an excellent workhorse of a writing program, designed for writing substantial works especially, but also good at ‘lighter bites’, like this post.
What I like, and what I found most helpful in my writing, is that individual sections, or chapters, can be separated into their own files ad hoc and ad libitum. The project itself, the program’s term for the whole, is actually a folder, ‘package’ in Mac speak, that contains all of these separate text files, with the ability to add research files, web pages, and other things too. Visible in the binder, these files can be opened in any combination by Scrivener, with side-by-side views, and moved about at will; all controlled, organised, linked, indexed, and referenced by Scrivener. There are more things you can do that might be helpful in certain situations too: index cards, and scriptwriting, among others. As I hinted above: this program is for writers generally, not specifically for academic writing, but it most certainly does not suffer from being a Jack-of-all-trades, as Word does.
Being able to separate descriptions as one bone per file allowed me to focus only on that; useful when some of these descriptions spread to over 1000 words each. Another important feature is targets, which kept me going with something to aim for both for the day, and for the whole project. You can even tweet your progress, should you wish to do so. I didn’t make my original deadline by a long way.
Of course, writing into this software is no different than any other designed for the purpose: keyboard, screen, time, will (not all of these are all present all of the time). However, it is the way in which the program allows you to work with what you’ve written, both during, and afterwards.
As Scrivener keeps each section in a separate file within the project, getting it out at the end requires the document to be ‘compiled’ from all the parts. This post-processing gives control over the look of the output. It might not be important for a single document that’s going to one place, but sometimes you might need to reformat it later. In essence, these compile settings act similar to text styles. They’re applied to both the body text, and to the subdocument headings, as defined. This latter is very useful for a multilevelled document. Numerous other features are available: the instructions are 540 pages long, and made in Scrivener itself.
Academic work has several hundred years of history behind it that must not be ignored, but instead must be brought in and included. Referencing the relevant previous work is just another potential headache, after finding and reading it in the first place. When this list of references becomes large, say 420 or so individual publications, help is very much appreciated. (This is the kind of number that many academics will have do deal with when doing their PhD thesis: perhaps the largest work in their careers.) I use two programs: Papers for Mac, to organise and view documents, and Bookends for Mac, to collect, insert, and format references.
Bookends for Mac by Sonny Software contains the best set of import, export, and customisation options for references that I’ve found. I’ve looked at EndNote, Sente, and Zotero, as well as the Citations function of Papers too. (I used to use Paper’s Citations when I used Pages, and wrote the first version of the style format for the journal Palaeontology in the Citation Style Language (http://citationstyles.org), which is used by Papers, Sente, and Zotero.) All of these allow you to change to format of both citations and the bibliography: which bits are included and their order, which are italicised or in bold, and so on. However, as many journals each have their own subtle differences in citation and reference formatting, it becomes difficult to cover all of these. (No reference assistant is perfect or complete, and most will require some tweaking at some stage.) Inevitably, it ends up being the small bits that are left over and have to be changed later: bibliography formatting is inevitably a time-consuming task. I’ve found that Bookends gives me those few more options, which that little less time having to be spent later: a generally more pleasant way to go.
Nicely, citations are easy to add with Bookends: simply import a citekey into the file from its database. The formatting stage comes later, by using the program to process the file, taking all the citekeys, formatting the citations, and adding a bibliography. As it is text based, this means that Bookends can work with files from many programs: simply export, format, import. There are also very useful options for showing only the date, or not having brackets around, for instance. I’ve found that doing my formatting in Mellel, which has particularly close ties to Bookends (they are available together in a discounted software bundle), adds a bit extra in formatting control, again saving that little, or more, extra time. While each of these savings may only a second or two for each edit, in such a long document, with several hundred or thousands of citations, that easily adds up.
Papers for Mac by Mekentosj, now part of Springer, is a document manager, primarily for pdfs. Import a pdf file and the software copies it to the library, and, for research articles, will automatically search for titles, authors, source, and other reference metadata. The program then lets you search through the text, view the document, highlight, add notes, and add associated documents. These are all immensely useful: the bread and butter of an academic’s daily work. Papers simply takes markup that was done on paper offprints into digital form. It is not the only such document organiser, Preview allows markup, other software organises files. Yet, being able to view, annotate, and organise articles, with the associated metadata, search, and citation tools is hugely useful.
Finalising for sending off
My workflow usually goes a little like this: write in Scrivener, export as Rich Text File (.rtf), import into Mellel, format references with Bookends, format paper as needed (this is usually minimal as Scrivener can generally cover all the bases), export as .pdf, preferably, or .doc/.docx to distribute. I needed to add an index, however, and Mellel, unfortunately, doesn’t have this ability. (It’s one of the things that has been requested in the forums, and this has been acknowledged by the developers, so it may appear.) For this, I tried importing into Word, but this struggled with indexing such a large document.
The process itself was simple: create a list of words to index, with how they should appear, make Word mark these in the document, add the index to the end. (I followed the instructions from Dummies.com.) Word struggled with this, although wasn’t beaten, but made working with the document afterwards difficult: pages appeared to be recalculated on-the-fly, so that’s something else that the program has to do. (I’m not sure whether this is actually how Word does this, but the constant slowness and crashing suggests that it was doing a lot of extra work once the index had been added.) It was too much: Word repeatedly crashed, and became frustratingly slow to use. I searched for an alternative.
I settled on Nisus Writer Pro for Mac by Nisus Software. It has the tools I need and works primarily with .rtf files, how I mostly pass through my writing. Using the trial showed me how useful Nisus Writer Pro is. It can do all the things that I need it to do, and quickly. Processing an index and creating contents does not take long: the compiling takes some time to go through, but the creating takes only seconds. (The process to create the index is the same as in Word.) Both of these are also stored as text to be updated as needed: on demand processing reducing the general overhead. The styles and formatting options are those typically found in word processors, but their implementation, their usability, and the way that they look, not an unimportant thing in my world, are more pleasant than many others. (I am somewhat of an aesthete.) Nisus Writer Pro can, conveniently, read the change tracking on Word documents, as can Mellel, perhaps the final part of working with documents. The realisation of this too is, I think, finer than in Word.
Microsoft Word is a powerhouse of a program, both in terms of functions, and ubiquity. I use it, when necessary. (I have signed up to Office 365 University, so get the benefit of the programs and OneDrive.) Yet I am increasing finding that I do not need to.
I use a MacBook Pro, running OS X. I have seen others complain about Word on OS X. I have not used Word on Windows. On that platform, it could be excellent and worth the share that it has garnered. If so, why not also on OS X? I do know that there are things supported by the Windows version that aren’t found in Word for Mac, certain advanced typographical options being the one I know best. These, specifically OpenType feature support, have only recently found their way into any version of Word. I’ll leave for now the discussion of word processing versus typesetting programs. Maybe the next version will allay my griefs. For the Mac version of Office, the time of this to appear is nigh.
I do not think that the way I’ve found myself working is bad though. Using several great programs that do what they do well has perhaps served me better than lumbering on with one that I disagree with. My experience has been far from a hardship, even with the program swapping and file manipulation.
I have had occasional problems, but the instructions that come with the programs are extensive, comprehensive, and useful; not all of those are guaranteed! Moreover, the forums (Scrivener, Bookends, Papers, Mellel, and Nisus) for each program are very helpful, and I’ve often been able to contact with the people who make these programs themselves.
Other blogs have talked about their experiences with these programs in their own projects. (In particular, I occasionally see posts about Scrivener appear in my Facebook feed: I follow them.) I urge you to look them up. Each has a trial option to, so why not try them. Some are cross-platform, and allow collaboration or working with documents as such, across many computers.
I don’t think there are many places to find how academics work. My immediate thought turns to the blog Academic workflows on a Mac by Aleh Cherp: on this blog, Aleh has reviews, thoughts, and personal workflows. This is a great place to see how things can work together to get things done. It may not suit everyone, not least because of the differences between research topics and methods. I’m curious whether anyone else has written about this, or what different processes other people use.
I haven’t posted anything here for a while: second year PhD syndrome has finally kicked in with a heavier work load. Hopefully this should ease a little towards and around easter. “But what am I doing”, I hear you cry?
I brief, I’ve been doing a lot of stuff on Ophthalmosaurus especially; visiting Peterborough Museum and extending my description etc. I’ve also looked at using morphometrics to quantify the disparity in this genus, Brachypterygius and others—I even have a poster on that to present today, although this is preliminary work.
Elsewhere, my time has been taken up with completing my phylogeny character list and playing in several concerts. On this topic: I’m excited to say that I’ll be playing tuba in Mahler’s Eighth Symphony, the ‘Symphony of a Thousand‘, in two weeks, probably the largest piece I’ll ever play.
So this is a brief catch-up, just to let you know that I haven’t forgotten you. Plans are afoot and gaining momentum. Until next time.
Twenty-twelve was a big year for ichthyosaurology. For me, it was my first full academic and calendar years as a PhD student at the University of Bristol studying ichthyosaurs. It also marks the 15th month of this blog’s existence and this will be the 35th post. That averages to more than one each month, which pleases me as there have been many occasions when I didn’t feel that I’ve lived up to my promises. Not that this means that I have.
So what about now? As this will be one of the first posts of 2013, why not cover some of my, and (mostly) others, work from the past year, as well as my plans for the next. Prepare to be dazzled!
Ichthyosaurs in 2012
The so-called ‘ichthyosaur renaissance’ is continuing in full swing with many people working on many exciting things. Last year saw new specimens unearthed and described, and at least five new species and three new genera named officially: Acamptonectes densus (Fischer et al. 2012), Stenopterygius aaleniensis (Maxwell, Fernández and Schoch 2012), Temnodontosaurus azerguensis (Martin et al. 2012), Cryopterygius kristiansenae and Palvennia hoybergeti (Druckenmiller et al. 2012). From all the research that came out last year, here’s a few pieces on some of the findings.
January was a bumper month, and great way to start the year. Erin Maxwell (2012a, b) published studies on the genus Stenopterygius from the Lower Jurassic Posidonienschiefer (Posidonia Shale) of southwestern Germany. Stenopterygius is certainly the most numerous and probably the most completely known ichthyosaur. Huge amounts of material have been found of this genus and now fill collections in the Museum für Naturkunde, Stuttgart, Urwelt-Museum Hauff in Holzmaden and many others besides. Examples can be seen in Heinrich Mallison’s recent post from his Palaeontology of SW Germany series. Having such an excellent record lends itself to detailed studies in the biology of Stenopterygius.
Species level metrics
Having so much material available frequently leads to an excess of enthusiasm in naming species, as has happened so often in ichthyosaurs. Maisch (2008) cleaned up the taxonomy of Stenopterygius into three species: S. quadriscissus, S. triscissus and S. uniter along with the erection of Hauffiopteryx typicus. The differences between these species are there, but are often subtle and depend frequently on the preservation – as in so many fossils. Using morphometrics – statistical variation in shape – Maxwell (2012a) showed that each species clearly occupies their own separate morphospace: each species is morphologically different (fig. 1). The area each species occupies on this graph also shows the variation within the species. S. quadriscissus is by far the most common and, as expected, shows the greatest variation, whereas S. triscissus and S. uniter don’t show as much. The effect of growth from juveniles to adults can also be seen: the four stars in the S. quadriscissus space mark two specimens of associated adults and juveniles. The large difference along the x-axis shows that size (mostly body length) dominates this variation, but that other changes (y-axis and other components) change noticeably too.
The Middle Jurassic (Aalenian–Callovian; 174–163 Ma) is largely devoid of ichthyosaur fossils worldwide. The Late Callovian Oxford Clay formation is full of Ophthalmosaurus and ichthyosaurs from the Bajocian–Bathonian (170–166 Ma) of South America are known (Fernández 1994, 1999). Stenopterygius aaleniensis (the ‘Aalenian Stenopterygius’) (Maxwell, Fernández and Schoch 2012) is the first conclusive remains from the Aalenian (174–168 Ma), not just of an ichthyosaur, but also of a marine reptile generally (i.e. plesiosaurs, pliosaurs and crocodiles too). This newly described specimen (fig. 2) is found in a similar area to those from the Posidonienschiefer, albeit in higher strata. The three-dimensional specimen has its head stuck out at a completely different angle to the rest of its body, giving a good all-around view; very important in ichthyosaur taxonomy, but made it difficult to incorporate in the two-dimensional morphometric study of the Posidonienschiefer Stenopterygius (Maxwell 2012a).
Cretaceous ichthyosaurs … “the Empire strikes back?”
That is the second part of the brilliantly titled article by Zammit (2012) looking at the diversity of ichthyosaurs in the Cretaceous. For a long time, there was only one genus – Platypterygius – to which almost all Cretaceous ichthyosaurs were assigned. Platypterygius currently contains seven or eight species because of this, although more have come and gone in the past. This is no longer the case: Platypterygius still dominates the diversity, and is in need of the same type of revision that Stenopterygius went through recently (Maisch 2008). However, now there are numerous other genera to accompany it.
This process began relatively recently, with the finding of Caypullisaurus bonapartei (Fernández 2001, 2007) and more recent reports have increased that with Maiaspondylus lindoei (Maxwell and Caldwell 2006b), Athabascasaurus bitumineus (Druckenmiller and Maxwell 2010), Aegirosaurus leptospondylus? (Fischer et al. 2011a), Sveltonectes insolitus (Fischer et al. 2011b) and Acamptonectes densus (Fischer et al. 2012). Along the way material and descriptions of Platypterygius have also been reviewed and revised (e.g. Fernández and Aguirre-Urreta 2005; Maxwell and Caldwell 2006a; Kolb and Sander 2009; Maxwell and Kear 2010; Adams and Fiorillo 2011; Fischer 2011; Pardo-Pérez et al. 2012).
Fischer et al. (2012) discussed the effect of this more recently realised diversity. Their elegantly simple graphs (fig. 3) show that there is low to no extinction in ichthyosaur species over the Jurassic–Cretaceous boundary (145 Ma). It’s also apparent that no new clades arose following the Kimmeridgian/Tithonian either. This implies one or two scenarios:
Late Jurassic and Cretaceous ichthyosaur lineages had extremely long lifespans.
The lineage and diversity data is incomplete, either due to incorrect assignment of species (lumping many together) or through incomplete sampling (no one’s bothered to look for any).
The latter of these is mentioned in the body text (Fischer et al. 2012, p. 22), with particular reference to the ‘wastebasket’ nature of Platypterygius and the poor rock record of the earliest Cretaceous. However, the conclusion remains: ichthyosaurs show stability in their diversity over the Jurassic–Cretaceous boundary and through the earliest Cretaceous. The age-old question of why they became extinct towards the end of the Cenomanian (94 Ma) stands.
A few new specimens
Along with Stenopterygius aaleniensis mentioned above, a few more ichthyosaurs took their turn in the spotlight. These add to our knowledge about the occurrences and biology these groups and the ecology they belonged to.
Ichthyosaurus communis finds are common along the coast between Lyme Regis and Charmouth (Dorset, UK); at least common for ichthyosaur finds. The preservation of the material can be spectacular – close to that seen in the Posidonienschiefer – but all too often it falls short. A specimen described by Bennett et al. (2012) does look a bit of a mess (fig. 4), but it’s still an informative mess! This specimen contains enough detail to be assigned to I. communis, making this the youngest definite example of that taxon. It was found in Pliensbachian age (191–183 Ma) rocks, whereas I. communis was previously known only from the Rhaetian–Sinemurian ages (208–191 Ma). There are also a number of fish remains preserved in the gullet region giving a glimpse of this ichthyosaur’s lifestyle.
The new species Temnodontosaurus azerguensis was named based on material from the Toarcian (183–174 Ma) of France (Martin et al. 2012). Again, this is another impressive specimen, for its preservation and its size, at the best part of 8 m long (fig. 5). The Toarcian is the age in which the Posidonienschiefer was deposited, making this specimen about, but slightly younger than the – three of the four – Stenopterygius discussed above. As Temnodontosaurus go, T. azerguensis is weird – which seems to be the fad for new ichthyosaurs nowadays: weird is good. There were no teeth found with the specimen and the snout is long and thin and with reduced dental grooves. This compares with the “large size … and massive dentition” (Martin et al. 2012, p. 1002) usually associated with Temnodontosaurus. Being from later in the Toarcian also means this ichthyosaur is from after the Toarcian Oceanic Anoxic Event. This ‘stagnation’ of the ocean occurs as oxygen levels in the ocean fall; fish and invertebrates then die and there is a bloom in decay bacteria, which then causes a further reduction in oxygen levels. An event like this leaves its trace in black, organic-rich strata, like the Posidonienschiefer. Few ichthyosaur remains are known from this time; whether this new species marks a post-event radiation cannot be determined.
While it may not be a new species, coverage of a Leptonectes with associated embryos is still exciting (Lomax and Massare 2012) (fig. 6). This was much closer to (my) home, being found only in Street (Somerset, UK), however the specimen is housed in the Sedgwick Museum, Cambridge; a little further a travel. Embryos have been known in ichthyosaurs for a long time (see this famous Stenopterygius (fig. 7)), but this is the first occurrence in Leptonectes.
The Upper Jurassic had a boost in attention towards the end of this year. I’ve covered the discovery of Cryopterygius kristiansenae and Palvennia hoybergeti in a post last year (Druckenmiller et al. 2012; ‘In the land of Svalbard…’). Also published was a description of some new material of Arthropterygius sp. from Argentina. Curiously, Arthropterygius was only previously known from Canada (Maxwell 2010) – several thousand miles away today, and not much less in the Jurassic. As shocking as this may seem, it isn’t unheard of: examples of Ophthalmosaurus are known the (western) world over; from England (Seeley 1874; Kirton 1983), Mexico (Buchy 2010) and Argentina (as Ancanamunia; Rusconi 1948; Kirton 1983; Fernández and Maxwell 2012). Modern Grey Whales also travel great distances – from their tropical birthing grounds towards the Arctic for feeding.
Besides naming new ichthyosaurs, a few papers discussed the palaeobiology of these animals both during life and after death. Rothschild, Xiaoting and Martin (2012) looked at decompression syndrome (‘the bends’) in ichthyosaurs from the Triassic in comparison to post-Triassic. Evidence for the bends can be seen in the state of the bones of ichthyosaurs: build-up of nitrogen in the bones blocking blood vessels and killing cells causes deformities (fig. 8). The findings show that Triassic ichthyosaurs – along with Stenopterygius – apparently lived a more sedate life than most of their Jurassic and Cretaceous relatives (see Rothschild, Xiaoting and Martin 2012, tbl. 1). The authors suggest several reasons for this increase in the bends in later ichthyosaurs:
Later ichthyosaurs, particularly the thunniform (tuna-shaped) group are more adapted to deep-diving so will be more affected by repeated decompression as they surface to breath (Motani, Rothschild and Wahl 1999).
Triassic ichthyosaurs dominated the top tiers of the food web whereas Jurassic and Cretaceous ichthyosaurs faced more predation from sharks, pliosaurs and marine crocodiles (Fröbisch et al. 2013).
Fast-swimming teleost fish evolved in the Late Jurassic and Early Cretaceous, which may have caused more accidental decompression in hunting. This may be associated with a more endothermic (‘warm-blooded’) metabolism (Bernard et al. 2010).
Incidentally, it was this article, along with its comments and replies (Hayman 2012; Rothschild 2012) that led to John Tennant at Green Tea and Velociraptors to write a letter.
Nakajima, Houssaye and Endo (2012, accepted and published online) gave more insights on early ichthyosaur biology. This study on Utatsusaurus hataii – one of the earliest and most basal ichthyopterygians – looked at the bone structure in the ribs and humeri of two specimens. The results suggest rapid growth and possibly raised metabolic rates: early in their evolution – and so soon after the Permo-Triassic extinction event (within 6–8 Ma) – these ichthyosaurs were already developing the characters that made them successful for 160 Ma. That Utatsusaurus had paddles and a long, finned tail was already known. The high growth and metabolic rates, along with spongy inner bone structure, hints at a pelagic (open ocean) lifestyle and palaeoecology.
To conclude the past year in ichthyosaur research, a look at their taphonomy. This takes us back, as has happened so often this year, to the Posidonienschiefer and exploding carcasses (Reisdorf et al. 2012). In recent years, the phenomenon of exploding whale carcasses has gained several hits, particularly from Inside Natures’ Giants and on YouTube (vid. 1). These incidences have led to the postulation that some of the scattered ichthyosaur remains found could be due to this cause (e.g. Böttcher 1989; Martill 1993; fig. 9). Explosions of carcasses in modern whales tends only to happen when there’s something around to disturb the carcass – frequently a person with a harpoon (vid. 1, fig. 10).
The carcass itself will tend to sink and – in deep enough water – the pressure will prevent explosion. The alternative mechanism Reisdorf et al. (2012) suggest is the sediments and currents. Slight currents would have been free to move the bones around in the nebulous ‘soupy substrates’ that made up the seabed (Martill 1993). Velocities of only 0.2–0.4 m/s (<1 mph; a very slow walking pace) would’ve be enough to move around the flank and belly ribs and the paddle bones causing such preservation.
This concludes my brief (really?) look at the published ichthyosaur research from 2012, but has not been comprehensive for the amount of research, or the summaries themselves. Twenty-thirteen has already seen ichthyosaur articles published (e.g. Fröbisch et al. 2013; Maxwell and Dececchi 2013), preview manuscripts (e.g. Nakajima, Houssaye and Endo 2012) and more that are currently in preparation.
I know what I did last year
From other peoples’ work to what I’ve been doing. As I began with, 2012 was my first full (calendar) year in my PhD and a year later I feel I’ve made progress: I’m almost getting to the results stage! My original plans (here, here and here) have changed somewhat due to feasibility, time and material constraints, but the gist remains the same.
The largest part of this year has been taken up with describing those ichthyosaurs from the Middle and Upper Jurassic. Fortunately, I was awarded several grants from the Palaeontographical Society, the Geological Society of London, the Systematics Association and the Bob Savage Memorial Fund. This money was spent between August and today on visits to various museums. My visit to Leicester received its own post, but I also went to the Hunterian Museum, Glasgow, Sedgwick Museum, Cambridge, University Museum of Natural History, Oxford and the Natural History Museum, London. I still have to visit Peterborough Museum in the coming weeks.
All this travelling was, for the most part, in search of as much of the material of Ophthalmosaurus from the Leeds Collections that I could find. I’ve only mentioned these collections briefly and they deserve to have more detail on them: one of my tasks for this year. All this travelling led me to over 300 specimens referred to Ophthalmosaurus, covering every (known) bone in its body (fig. 11).
In some select places, particularly the Natural History and Sedgwick museums, there were those more elusive treats Brachypterygius and Nannopterygius. In Cambridge, I came across the giant skull originally named Grendelius (fig.) and London has the difficult to see skeleton of Nannopterygius (fig.) This last is still causing me access problems due to its position (~6 m up on a wall), but this should hopefully be resolved later this year.
The descriptions of these three ichthyosaurs are largely complete in draft form. The basis was taken from Kirton (1983), as I’ve mentioned before, and I’ve checked and added much to it. Much that now needs to be done revolves around editing this into a manuscript, and writing the introductory and discussion sections.
When I haven’t been doing stuff with ichthyosaurs descriptions, I’ve been working on their relationships. This is continuing as originally planned, and I now have a set of characters and the first stages of a matrix, which is progressing well. The collection, comparing and construction of this has been time consuming because it requires detailed qualitative understanding of the ichthyosaurs themselves (all 101 species, and counting) and the characters themselves. Because the characters I’ve collected are derived from several sources, their purposes and nature can be very different. These wrinkles have to be resolved before any analysis can take place; this is where I am now.
Other odd jobs
Much of the studies that I wrote about in ‘My PhD: Part 3’ require a complete, robust phylogeny; hence have not been properly started yet. It is also here that some of the greatest changes have happened. I had hoped to use some three-dimensionally preserved ichthyosaur skulls (e.g. those from Caine and Benton 2011), CT scanned, as the basis for a finite element analysis of their jaw mechanics. Unfortunately, due to the complexity of the skulls (50+ elements), the problems of modelling sutures (where these elements meet) and it taking a long time to build these models, it doesn’t seem feasible to do this (yet).
Instead, following the suggestion of one of my supervisors, Emily Rayfield, I’ve been looking at the related modelling of fluids (computational fluid dynamics). The idea with this will be to use two-dimensional body silhouettes to look at the efficiency of ichthyosaurs’ motion through the water. This is very much in the designing/planning/guessing stage. I’ve run some preliminary simulations (fig. 14) just to look at how, and if, the model works. Next will be to compare with flume experiments (e.g. Ferry and Lauder 1996) to make the results are realistic. Eventually this can be combined with the phylogeny to see if there are any trends through ichthyosaur evolution.
Outside of my research, 2012 offered the chance to go to several meetings:
Big Palaeontology was this year’s Lyell Meeting at the Geological Society (29 March), featuring talks on topics ranging from specimen databases and virtual palaeontology through to fossil code and palaeontology of the Jurassic Coast World Heritage Site.
So what does the year ahead hold for me? Currently I’ve spent the best part of the last month not writing this blog post, and the last two days writing all 3000+ words of it, which has been good for affirming my ability to write (the amount of editing and making images notwithstanding). As last year had much work on the descriptions of Ophthalmosaurus, Brachypterygius and Nannopterygius, this month I’ve largely put that aside, until after visiting Peterborough. On the other hand, I am in the process of writing a proposal for a Society of Vertebrate Paleontology Memoir I’ve looked at many places to publish, with the criteria of quality, circulation and accessibility (not in that order). PLOS ONE looked promising (thanks to Darren Naish for the suggestion), but unfortunately they just won’t accept monographs (large, complete bodies of work, which this will be). The SVP memoir series offered the best mix of these three criteria; should it be accepted, it will come out in 2014.
I have however picked up on creation the character list and matrix for my phylogeny, looking to complete this within ~two months. So many other things will be born from this and take up so much of the rest of my year – a flurry of projects, as I like to think of it.
With all this work going on and (hopefully) being completed, 2013 is looking like a busy and rewarding year. I am expecting to have my first peer-reviewed publications, first conferences talk(s) and poster(s) and be largely on the way to completing my PhD.
HAYMAN, J. 2012. Deep-diving dinosaurs. Naturwissenschaften, 99, 671–672.
KIRTON, A. M. 1983. A review of British Upper Jurassic ichthyosaurs. Unpublished PhD Thesis, University of Newcastle-upon-Tyne, Newcastle-upon-Tyne, 239 pp., 45 figs., 5 pls.
KOLB, C. and SANDER, P. M. 2009. Redescription of the ichthyosaur Platypterygius hercynicus (Kuhn 1946) from the Lower Cretaceous of Salzgitter (Lower Saxony, Germany). Palaeontographica Abteilung A: Paläozoologie—Stratigraphie, 288, 151–192.
LOMAX, D. R. and MASSARE, J. A. 2012. The first reported Leptonectes (Reptilia: Ichthyosauria) with associated embryos, from Somerset, England. Paludicola, 8, 263–276.
MAISCH, M. W. 2008. Revision der Gattung Stenopterygius Jaekel, 1904 emend. von Huene, 1922 (Reptilia: Ichthyosauria) aus dem unteren Jura Westeuropas. Palaeodiversity, 1, 227–271. [In German.] 🔓
MARTILL, D. M. 1993. Soupy substrates: a medium for the exceptional preservation of ichthyosaurs of the Posidonia Shale (Lower Jurassic) of Germany. Kaupia, 2, 77–97.
If you’ve followed dinosaurpalaeo like I have, you’ll have seen Heinrich Mallison’s continuing series on the palaeontology of SW Germany. The latest instalment, published last week, features the ichthyosaurs of the Posidonienschiefer, as held in the Hauff Museum, Holzmaden, Germany. These are some of the best preserved ichthyosaurs in the world, and Heinrich’s photos are excellent. It’s well worth a look.
Also, for those who remember, I promised a review of last year in my life and ichthyosaurology. This is in the works, but there was a lot of news and research to look at. All that I can say is: watch this space!
You’re in for a BIG surprise! We may only be in the third week of 2013, but already there’s some exciting news on the ichthyosaur horizons. Last Monday (7 January 2013) came the exciting news of a new macro predator; because adding ‘big’ to the front of ‘predator’ just makes it more awesome.
So what have we got here. The name pretty much says it all: Thalattoarchon saurophagis, the ‘reptile eating ocean ruler’ (Fröbisch et al. 2013), it doesn’t run off the tongue, but a little skip isn’t too bad.What we have here is a big and mean beast that could probably have eating most of the animals around it. There are several reasons why this find is odd and important: first, how is different to other ichthyosaurs?
Om nom nom
Thalattoarchon is a big ichthyosaur, estimated to be at least 8.6 m. This is a similar size to the Late TriassicCymbospondylus and as big as the largest Temnodontosaurus from the Early Jurassic. (It does pale in comparison to the largest Shastasaurus [~22 m], but they’re likely in completely different ecologies.) Thalattoarchon has a skull that is around twice the size of a similarly sized Cymbospondylus, and the skull is the real business end.
In the mouth you find many teeth. With Jurassic ichthyosaurs, I’m used to dealing with teeth that are a few centimetres long, about one centimetre across and very smooth all over. Thalattoarchon had big teeth, more than 12 cm for the largest, and these weren’t smooth; they were equipped (in life) with a pair of sharp slicing edges. This condition is called bicarinate, literally ‘two-keeled’. It’s found in a few groups, such as in the crocodilian Rimasuchus, and the mosasaur Hainosaurus, but infrequent in ichthyosaurs. Some examples of Temnodontosaurus platyodon have them as does the enigmatic Himalayasaurus tibetensis. The shape of the teeth puts it in the ‘cut’ group of Massare (1987).
So what’s so special about this beast, other than it’s a large, predatory ichthyosaur with big cutting teeth? Really, you need more than that?
Besides being a macropredator, Thalattoarchon saurophagis has the distinction of being one of, if not the, earliest macropredatory tetrapods in the oceans. Tetrapods are vertebrates that have four limbs, a group made up of amphibians, reptiles, birds and mammals, plus a few others. This notably excludes the fish, which don’t have limbs, but have many fins instead.
Nowadays, there are two animals that hold the top rung in the oceanic food chain, the Orca or Killer Whale (tetrapod) and Great White Shark (fish). In the Cretaceous there were the mosasaur Tylosaurus (tetrapod) and the ‘bulldog’ fish Xiphactinus. Xiphactinus has been made famous by the ‘fish in a fish’ fossil: a Xiphactinus was killed eating a fish that was too big. The Jurassic had the pliosaurs Pliosaurus and Liopleurodon (both tetrapods), which wasn’t the 25 m in length that Walking with Dinosaurs suggested, although others may have come close. And the Triassic had Thalattoarchon. But what about before then?
Despite there being about 300 million years before Thalattoarchon, and there being tetrapods for ~100 Ma of that, the main threat in the oceans then were big fishes. The meanest looking was Dunkleosteus, not just because it was up to 10 m long, but also it’s head was covered in thick bony plates, and its mouth full of slicing bony plates too. The Devonian (419–358 Ma) is famous for its placoderms, to which Dunkleosteus belongs, the armoured fishes that specialised in bony defence across their bodies.
All change at the top
The appearance of Thalattoarchon saurophagis marks a change from the fish-tipped Palaeozoic food webs to the Mesozoic and Cenozoic (including today) tetrapod-dominated oceans. The end of the Permian (252 Ma) was marked by the largest mass extinction known; a frequently quoted figure is 95% of life in the oceans died out. Thalattoarchon is from rocks deposited at least 244 Ma, within 8 Ma of the Permian–Triassic boundary, and only 4 Ma from the earliest known ichthyosaurs (Thaisaurus and Utatsusaurus; Shikama, Kamei and Murata 1978; Mazin et al. 1991; Nicholls and Brinkman 1993). This is a very rapid diversification to occupy these vacant niches. The Triassic in general was an exciting for all marine animals to spread and colonise new areas, the weirdness of early sauropterygians is a good example.
MAZIN, J.-M., SUTEETHORN, V., BUFFETAUT, E., JAEGER, J.-J. and ELMCKE-INGAVAT, R. 1991. Preliminary description of Thaisaurus chonglakmanii n. g., n. sp., a new ichthyopterygian (Reptilia) from the Early Triassic of Thailand. Comptes rendus de l’Académie des sciences. Série 2, Mécanique, Physique, Chimie, Sciences de l’univers, Sciences de la Terre, 313, 1207–1212.
SHIKAMA, T., KAMEI, T. and MURATA, M. 1978. Early Triassic Ichthyosaurus, Utatsusaurus hataii gen. et sp. nov., from the Kitakami Massif, Northeast Japan. Science Reports of Tohoku Univeristy, Second Series (Geology), 48, 77–97.