Friday, August 30, 2013

Photography experiment with fur seal crania

Ewan was pretty excited because today we received in the mail two LED photo floods that can be used for fossil photography. I decided to try one out, as I needed to photograph some NZ fur seal skulls, mandibles, and teeth which Carolina Loch recently prepared from fleshy, stinky heads. We use a sheet of somewhat opaque plexiglass that can be backlit with a small floodlight, which burns out the background making photo and figure editing quite a bit easier, in addition to giving photos a nice "glowy" or luminescent feel to them. Aside from this, we also use two large floodlights and a set of diffusers to create soft lighting. Ewan is an expert in fossil photography and there are hundreds of small tips he has, and all sorts of home-built tools and gadgets to prop specimens of any shape up in just the right position.

The juvenile NZ fur seal (Arctocephalus forsteri) mandible under normal photographic conditions, with the dentition removed.

The nice thing about a small LED photo flood is that it can go directly under the plexiglass plate, directly backlighting the specimen you're going to photograph. When I placed a fur seal mandible directly over the LED, it actually shone right through thin parts of the bone - and this actually allowed me to see the outline of the tooth sockets (alveoli). This is pretty interesting, because normally to get an image like this in lateral view you need to take an X-ray; unfortunately, since fossils are filled up with all sorts of other crap like sediment and calcite, this method won't work on fossils. In fact it won't even work for some modern specimens, and it is likely only useful for very thin bones. In a way, it is somewhat analogous to an X-ray: the photograph is capturing radiation that is able to pass through thinner (and presumably lower density) parts of the bone. In this case, it's not strictly following bone density as it is following bone thickness - but that's a minor point I concede, as it still results in a similar looking (and informative) image for my purposes.

 Right mandible of juvenile NZ fur seal (Arctocephalus forsteri), showing the alveoli; 
lower photograph is slower shutter speed.

Then I got to thinking, what else can I show with this? I took one of the two skulls and turned on the LED light, and found that it would indeed show some of the brain surface topography that is imprinted on the endocast of the skull. I've got some more photos, and it turned out quite well I think. Now, I'm not sure what sort of practical application this could have other than being a cheap alternative to X-rays in somewhat rare cases like this, but maybe somebody will think of some useful way to use this for delicate osteological specimens.

 Illuminated braincase showing some impressions of sulci and gyri.

Tuesday, August 20, 2013

Day trip to the Otago Peninsula (finally)

Even though we've been living in New Zealand for over a year, everyday groceries are shockingly expensive here and we haven't really been able to afford any luxuries like leaving town. With Morgan and Josh in town, we were able to borrow a car from our labmate Tsai and split the gas (for an hour and a half of driving, it was about 45 bucks or so to fill back up; that's 30 cents gone every minute - there's a reason Sarah and I won't be buying a car while we're down here!). So, we picked up the car from Tsai, hopped in, and headed out to the Otago Peninsula for a day to go try and see pinnipeds, penguins, and albatross.

We saw some pukekos in a field past Portobello, which is one of my wife's favorite birds - they are really pretty, and a bit awkward in proportion that gives them some real character.

We saw some oystercatchers down at Pilot Beach, which at dusk is a good spot to try and see little blue penguins.

At Pilot beach there was also a nice paradise duck fly by.

A New Zealand fur seal (Arctocephalus forsteri). I had seen these on a previous field trip to Wangaloa.

Some more fur seals at Pilot Beach.

Up the hill at Taiaroa Head, a single cormorant flies out to sea.

A spotted shag (a first for me) flies low over the Pacific.

A spotted shag unsuccessfully tries to land on a vertical face at Taiaroa Head.

These two NZ sea lions (Phocarctos hookeri) battled for about a half hour when we got to Sandfly Bay.

Sea lion combat at the east end of Sandfly Bay.

A lone sea lion emerges from the surf.

The two subadult males continue to fight (they must have raging testosterone levels).

An old adult sea lion growls at a younger male.

The old male had an impressive yawn.

The view east along the harbor just after sunset.

The view west towards Dunedin from the peninsula just after sunset.

Monday, August 19, 2013

Farewell to Morgan Churchill (EAPSI), and welcome to our newest labmate

July and most of August have come and gone, and along with them so has Morgan Churchill's EAPSI (East Asia Pacific Summer Institute) visit to Dunedin. Morgan visited to study the fossil sea lion Neophoca palatina, originally described by Judith King in the early 1980's from the Pleistocene of Ohope on the North Island. Morgan's project, to which I am attached as a coauthor, is threefold: 1) reevaluate and rediagnose the fossil species (e.g. does it really represent a distinct or extinct species within Neophoca? Neophoca today only lives in Australia), 2) collect a large volume of measurements for morphometric analyses of skull shape in otariids to quantitatively evaluate where Neophoca palatina belongs, and 3) get the holotype on loan so we can reassemble it and study it directly, rather than just a cast (the holotype was significantly damaged when it was transported back to New Zealand).

Morgan Churchill examines fragments of the Neophoca palatina holotype as we begin to reassemble it in the OU paleontology lab.

Morgan flew out about two weeks ago, and successfully completed all of the goals of his visit - he spent about tree weeks out of the trip in Australia and north island collections, measuring modern otariids. He was rather surprised at the rarity of NZ sea lion specimens in NZ museum collections; in the US we have programs where virtually every reported pinniped and cetacean stranding is collected for osteological collections, as a direct consequence of taking necropsies. My impression is that such a comprehensive system is not in place here. Regardless of a small sample size for Phocarctos (NZ sea lion), Morgan's data set already has some intriguing results.

About a week before Morgan flew back to the US, our newest member of the lab flew to Dunedin to begin his Ph.D. with Ewan. Josh is a former student of Robin O'Keefe, who works predominantly on marine reptiles at Marshall University in West Virginia; Josh is an Illinois native, and did his master's thesis at Marshall on functional morphology and locomotion in basilosaurids and other cetaceans. He's the second student to have started after me (Tsai being the first). Josh's dissertation will focus on describing numerous new kekenodontid fossils from the Kokoamu Greensand and Otekaike Limestone - possible Oligocene relict archaeocetes (which previously includes only two described fossil from New Zealand, Kekenodon onamata, and "Squalodon" gambierensis). So, welcome Josh! It is damned nice to have another American in the office, and it's nice to have a drinking buddy now.

A terrible photo of Josh Corrie at Sandfly Bay, taking photos of NZ sea lions (just out of camera shot). It's actually a fine photo (my wife took it), but none of the photos from the Otago Peninsula (or from fieldwork last week) show anything but his back, since I was typically hiking slow and taking too many photos.

Saturday, August 17, 2013

Fossilized ambergris from the Pleistocene of Italy: tales of marine taphonomy 1

I’ve wanted to somewhat regularly cover marine taphonomy on this blog for a while now, and with the recent publication of Baldanza et al. (2013), I thought that now is as good a time as any to start. It’s been a pretty busy last couple of weeks, but I’ve just delivered a department talk and have also spent the past few days recouping from a nasty cold, and now have some spare time again. So, here's installment 1 of a new series, tales of marine taphonomy. I'll occasionally cover papers discussing some of the weirder and less familiar aspects of marine taphonomy - and the taphonomy of marine vertebrates in particular. To be honest, it's not a subject that has been given much attention any way (so many "regular" concepts will probably be foreign to terrestrial workers), and many studies have butchered the subdiscipline altogether.

The last couple of weeks have seen some exciting advances in paleontology, but while everyone on the paleo-part of the internet was busy discussing the two papers reporting on new Jurassic mammals – in the same issue – but disagreeing whether or not they were mammals or something further down the stem – a new discovery was published that is actually interesting (and not just controversial from the standpoint about cladistic disagreements, which – no offense – can be horribly dull). Fossilized ambergris was reported by Baldanza et al. (2013) in the journal Geology from the Pleistocene of Italy. This is pretty damn neat, as it’s something I never had much hope in being preserved in the fossil record.

An atrociously humongous slab of ambergris. From

First off, what is ambergris? Ambergris – or gray amber – is a waxy substance formed from bile secretions in the digestive tract of sperm whales. It is often found with embedded squid beaks, and is thought to be a sort of protective lining that forms along the sides of the intestinal wall to protect against the sharp beaks. Ambergris can be expelled as fecal matter, or if too large it may be regurgitated. In the days of whaling, ambergris could be found within the intestines of freshly killed whales. It is often picked up by beachcombers along the shoreline (and beachcombers often pick up all sorts of other goodies that they think is ambergris). Ambergris is buoyant, and will float all the way to shore. Unlike cetacean feces – which has the consistency of greek yogurt and rapidly disaggregates once pooped out – ambergris is formed as somewhat consolidated chunks. Ambergris is perhaps most famous for its smelly qualities: although the soft, fatty and white precursor to ambergris (unsurprisingly) retains a strong fecal smell (how pleasant), once aged properly (apparently by sustained floating in the ocean) it can become quite hard and will produce a sweet smell, often compared to rubbing alcohol. The smell itself is of course not fantastic or of serious note, but it is rather its potency as a fixative for odors that makes it desirable for perfumes. It’s currently illegal to own or sell ambergris in the United States, and has long been rendered obsolete by synthetic fixatives; it is still possible to find perfumes made with ambergris in some European countries.

In their new paper, Baldanza et al. (2013) report about 25 coprolites from early Pleistocene (~1.75 Ma) marine rocks in Italy. These coprolites were calcareous, equidimensional to oval/lozenge shaped, up to 1 meter in length, and discolored relative to the background sediment; they were found to occur within only ~1200 square meters. A series of concentric ring traces are present, which argues against these structures representing things like recently described lungfish burrow traces. Occasionally, some specimens showed longitudinal wrinkles, which in modern in situ ambergris specimens occur on conical parts tapering towards the anus. Most damning of all, many of the coprolites were filled with squid beaks – oddly enough, mostly lower beaks, and upper beaks were rare and poorly preserved. Several chemical analyses were undertaken, and liquid chromatography analysis detected the presence of lipid derived organic compounds, and cholic acids which might be related to mammalian gastric activity were also found. Traces of eight amino acids were also detected, and relate to the decomposition of squid beaks.

Some ambergris coprolites - from Baldanza et al. (2013).

Some interesting hypotheses have been proposed to explain the occurrence of these ambergris coprolites. What’s strange is that they all occur in a single stratum in a small area (1200 square meters – approximately 35 by 35 meters, or just less than ¼ the area of an American football field), which is a pretty high density of ambergris. Baldanza et al. (2013) argued that their ambergris masses represent remains present within dead sperm whales, rather than coprolites naturally excreted in life – although, based on what information, I am unaware. Baldanza et al. (2013) suggest that the presence of whale fall mollusks in the vicinity are suggestive of a mass mortality event – and the carcasses were apparently preserved elsewhere. They further suggested that the paleogeography of the area may have served as a ‘natural trap’ for pods of sperm whales pursuing squid into shallow waters.

Some more ambergris specimens. From Baldanza et al. (2013).

I am certainly happy with the discovery of fossil ambergris – that is surprising enough. However, I don’t really think it’s at all necessary to invoke some sort of catastrophic interpretation for an assemblage that cannot really even be called a death assemblage, because there isn’t any evidence of death. There aren’t even any skeletons – the analogy would be digging up a vault toilet at a summer camp and identifying it as a mass grave. If there’s no body, it’s hard to claim that a murder has taken place. What mechanism would there be for removing the skeletal remains, but leaving instead coprolites with a far lower preservation potential? I can’t really think of one, save for a bunch of whales defecating at death and having the presumably easier to transport ambergris chunks transported elsewhere on the seafloor.I think a far more plausible hypothesis would be as follows: the locality was sort of a paleogeographic ‘eddy’ where ambergris floated and concentrated by surface currents, eventually becoming waterlogged and sinking to the seafloor.

Now, why was I never very optimistic about cetacean coprolites? Here's a youtube clip showing what happens when a dolphin defecates (it's not really that gross):

Ambergris, on the other hand, is a bit more cohesive and solid, so to speak. It probably won't be so diffusive upon its exit from the body. What hopes can we have for finding ambergris in older parts of the rock record? It mostly rests on two questions: 1) is ambergris restricted to the extant sperm whale Physeter? and 2) how far back does the fossil record of Physeter extend? According to Rice (2009), the answer to the first question is 'yes'. Answering the second question is a bit more difficult, as Physeter doesn't really have much of a fossil record, although Physeter-like sperm whales were around during the early Pliocene (Whitmore and Kaltenbach 2008), and a close relative that already had adaptations for teuthophagy is known from the middle Miocene of California (Aulophyseter).

Baldanza, A., Bizzari, R., Famiani, F., Monaco, P., Pellegrino, R., and Sassi, P. 2013. Enigmatix, biogenically induced structures in Pleistocene marine deposits: a first record of fossil ambergris. Geology doi:10.1130/G34731.1
Rice, D.W. 2009. Ambergris. Encyclopedia of Marine Mammals, 2nd addition. p.28-29.

Whitmore, F.C., and J. A. Kaltenbach. 2008. Neogene Cetacea of the Lee Creek Phosphate Mine, North Carolina. Virginia Museum of Natural History Special Publication 14:181-269

Friday, August 16, 2013

For the love of science, the pygmy right whale was NOT originally thought to have gone extinct 2 million years ago!

While I have not yet seen the fake documentary “Megalodon: the monster shark that lives” which has put yet another nail in the coffin of the discovery channel’s reputation for quality programming (what with shows like Moonshiners, Amish Mafia, Auction Kings, Pot Cops, and Weed Country – among others), I have heard that the show has inaccurately reported research from our lab here at Otago in order to support bogus claims that C. megalodon still exists. Now, it’s also important to note as a disclaimer for the uninitiated that the writers never intended their show to be taken at face value as anything but a fake documentary – although it is hardly forgiveable that it was not marketed as such, and that there wasn’t any “WARNING: TOTALLY FAKE” or “100% FANTASY” disclaimer at the beginning of the show.

I won’t be getting into any of the details about C. megalodon survival or other shortcomings of the show, for two reasons: 1) I will discuss the former when it’s appropriate, as I have a paper in preparation on the subject (or rather, the timing of the extinction) and 2) I haven’t actually seen the fake documentary and it would be pretty tacky of me to further rake the muck, and others such as Brian Switek have done a good enough job already (Here and here).

On another note, it is pretty depressing to see what the Discovery Channel has devolved into: the same kind of reality show crap that’s on A&E and The “Learning” Channel. When I was a kid I couldn’t get enough of documentaries with all sorts of beautiful shots of things like reef fish, big cats in their native environment, reptiles in the desert in Africa, and sharks and whales in the open ocean. I ate that stuff up. Nowadays, all it seems like you get on DC is a bunch of rednecks in the swamp, forest, or Alaskan tundra. So many of these shows are deliberate knock-offs of deadliest catch, which I’ll admit can be mildly entertaining. At least Mythbusters and Dirty Jobs, while technically are of the reality show strain, are genuinely aimed at being educational and happen to be really entertaining; however, all of these other Deadliest Catch clones are 5% education, 95% dramatized BS.

Caperea, the baleen whale that, according to the Discovery Channel, was recently rediscovered and formerly thought to be extinct since the Pliocene. 

Okay, rant over, now for some (real) science. In the show, numerous lines of evidence were touted (or completely invented) to indicate that C. megalodon was not in fact extinct, but was still very much alive. One of these arguments was the ‘fact’ that the pygmy right whale (Caperea marginata) had been thought to be extinct for the last two million years and was recently ‘rediscovered’ – which suggests that relatively large bodied marine vertebrates in the open ocean can go undetected, and contribute to someone’s hopes that such a monster as C. megalodon might have survived. However, this is so patently false it’s absurd, and I have a good idea where this misleading tid bit originated from. I mean, the claim is just so... odd that if it weren't a misrepresentation of my lab's researcg, it would be hilariously befuddling. Some of what follows is going to be a brief re-tread of some previous posts on the pygmy right whale I’ve done, so I’ll be brief. Here are a list of things we actually know, written in order so as to tell the story of how the writers got it so damn wrong:

1) The pygmy right whale did not have a published fossil record until 2012. Neobalaenids were not known from the fossil record – at all – until a fragmentary earbone was published from the late Miocene of Australia (read about it here), and a nearly complete skull was published from the late Miocene of Peru (Miocaperea: read more here). This disproves the argument that Caperea was long known only from a Pliocene, pre 2 Ma fossil record. In fact, the fossil record of Caperea has only been known to science for about 11 months.

The skull of Miocaperea pulchra, one of two published neobalaenid fossils. The pygmy right whale fossil record did not exist in the published literature until 2012 (contra the Discovery Channel).

2) Caperea has been known about since the 19th century. It was encountered during southern hemisphere voyages in the 1830’s and 1840’s. Sure, it is a poorly known extant whale – but it is far better known than many ziphiids, some of which are known from thin threads of recorded data. It, however, is by no means anything close to what you could call a cryptid or anything marginally close to a rediscovered ‘living fossil’ like the coelacanth; it was known in the flesh for a century and a half before it ever had a fossil record, quite the opposite of the claim in the show.

3) Caperea has recently been reinterpreted as a member of the family Cetotheriidae, based on phylogenetic research by my adviser, R. E. Fordyce, and fellow labmate Felix Marx. The Cetotheriidae were formerly known only from the fossil record, and were known – at the time of their writing – to have a fossil record as young as about 2 Ma, based on the youngest fossils of my favorite whale, Herpetocetus. Subsequent work published by myself earlier this year documented Herpetocetus surviving as late as the middle Pleistocene (~1-0.7 Ma). This effectively means that Caperea has been transferred in terms of familial placement – i.e. it’s a cetothere rather than a member of the (formerly) monotypic Neobalaenidae. This obviously doesn’t change the status of Caperea as far as extinctions go; it still has a shitty fossil record, although it’s now identified to be more closely related to a group with a decent fossil record.

Which brings me to point 4) When the Fordyce and Marx phylogeny was published, the LiveScience press release ended up with a pretty misleading title: “Found: Whale thought extinct for 2 million years”. The rest of the article is fine, and accurately describes the research, but I don’t know what happened with the title. When you search on google for details about that research, that article comes up, and I believe that this poorly titled press release happens to be the origin of the “Caperea was thought to be extinct!” myth cited on the fake documentary.

So there you have it. The writers must have seen that press release and latched onto that as gold, to the exclusion of all the good, accurate information on the web regarding the pygmy right whale. Oddly enough, a I wrote a decent synopsis of the research here on my blog (see here), and had the writers of the show bothered to read it, the published article, or even the rest of the mis-titled press release, this misrepresentation of our lab’s research could have been totally avoided.

For more on Caperea:

Wednesday, August 7, 2013

Otago Peninsula preview

Two weekends ago my labmate Cheng-Hsiu Tsai (nickname Tsai) lent us his car for a day so that I could drive Sarah, visiting EAPSI student (and coauthor) Morgan Churchill, and new labmate Josh Corrie out to the Otago Peninsula. Sarah and I don't have a car here, and can't really afford to rent one. So this was a great opportunity, and we saw a lot of great stuff out there (sadly, no penguins though). On the way back, I took a large panorama from the peninsula looking back west along the Otago Harbor:

(Click for mega-size)

The mountain on the right is Mt. Cargill, and the bright white light left of center is the Forsyth stadium; the black patch to the right of it is Signal Hill, with the lights of Ravenbourne below. Dunedin is obvious all the way to the left, and on the right extreme is Port Chalmers.

More photos are coming soon!

Sunday, August 4, 2013

A new Pelagiarctos specimen, part 2

 After the test casts with dental plaster turned out pretty well, I knew the mold would be well-suited to move on and upgrade to resin. In our lab in the geology dept. we have laminating resin, which works best in thin coats; it reproduces fine details excellently – but if poured into a thick, solid shape, it can crack from expansion during the curing process. With small molds – this one for example required about 5ml of resin or plaster – it won’t expand enough to crack.

Pouring resin is a bit less friendly than plaster – it irritates the eyes, and is harmful if inhaled, and the catalyst is even worse on both counts. Because of these issues, goggles, a respirator, and gloves are necessary (and a labcoat, of course). Pouring resin takes a number of mostly simple steps. First, removing any remaining resin fragments from the last pour is a necessity. A cheap cup can be used on a scale which reads to the hundredths place (and expect it to get messy - you will drip resin and silicone during mold making onto the scale), and make sure to tear off. The appropriate catalyst needs to be measured in tiny increments, and if you need under 10ml, you’ll be able to count the number of drops of catalyst going into the cup. Too much catalyst – particularly for batches of resin over 10-20ml – and the mixture will heat up and potentially catch fire.

Freshly poured resin cures in the mold.

After pouring the resin, carefully mix (so as not to introduce air bubbles) with a popsicle stick or tongue depressor, and then mix in any pigment (otherwise, the cast will be slightly translucent; surface details will be less evident unless a solid color pigment is mixed in). When mixed, two techniques can be used for filling the mold: a straight pour, or a thin layer can be painted into the mold. Painting a thin layer was necessary in order to fill all the cusps at the base of the crown of this tooth. After the cast is poured, it will take about 45-60 minutes to cure. After about 30-45 minutes, it will be solid enough to remove; if it is still warm and slightly pliable, then trimming it with an X-acto knife will be possible (and next to impossible if it is totally cured). However, if it is too pliable, then holding the cast while trimming it can leave imprints of your fingerprints in the resin.

After a couple weeks of molding and casting, now I have more than ten high quality casts of the Pelagiarctos tooth. I’ll be able to send the mold and the original specimen back to Wyoming, and casts to numerous institutions including UCMP (Berkeley), the LA County museum, Cooper Center (Orange County), San Diego Natural History Museum, Smithsonian, and probably the National Museum of Nature and Science in Tokyo (pretty much to any museum where fossil walruses – or walrus researchers – exist).

Unfortunately I don't have any more photos from the casting process; your gloves tend to get pretty sticky from resin and catalyst, and I wouldn't bother ruining an expensive camera just so you guys can have a couple extra photos (no offense). Anyway, here's the finished product - two test casts and a bunch of resin casts (there are even more now).

This isn't the end of the molding and casting, however; we've gotten a hold of a modern New Zealand sea lion skull, currently loaned to us from Steve Dawson over in Marine Sciences, who has graciously allowed Carol to take a premolar and section it (for science). With this, we'll have teeth of the NZ fur seal (Arctocephalus forsteri) and the sea lion (Phocarctos hookeri) for SEM comparison with Pelagiarctos thomasi. Steve knew that we have the capability of making high quality molds and casts, so he said it would be alright if we molded and casted the tooth first. Here are some photos from the second mold.

Silicone is poured into the acetate dam, around the tooth. Trust me, it's buried in there.

We're left with a solid cylinder of silicone with a tooth buried in the middle, and a 
clay plug on one end.

An X-acto knife is used to make a planar cut so that the mold can be split and the tooth (and later, casts) can be removed. In order to cut everything, the two halves can be gently pulled apart in order to see the remaining uncut portions of mold. It's probably important to be careful here and not end up with a ragged seam line, as that can add quite a large amount of 'flashing' (paper-thin amounts of resin that fill in the seams, which you can see on plastic model parts and cheap green plastic army men).

The clay plug is removed... show the root of the tooth.

And Voila! The tooth is removed, with a great mold left. I've made several casts of this 
specimen and they've all turned out great.