Monday, December 5, 2016

"No, you don't have a Prosqualodon tooth" and other common myths and misconceptions about fossil cetaceans

Within the world of paleontology there is on occasion a disconnect between the names, ideas, and concepts embraced by academics and amateur fossil collectors. Some of us academics do our best to educate the community, and others make little attempt. The purpose of this post is to clarify several commonly believed ideas I've heard amongst fossil collectors, but evidently have either been discounted within the peer reviewed literature or originated completely outside the world of academic paleontology. I jokingly refer to these sorts of ideas as "fossil folklore"; a very, very common version of this is "I knew a guy who found an 8 inch long megalodon tooth" (they rarely exceed 6.5 inches and do not really exceed 7) and every Miocene shark tooth locality I've ever been to has an apocryphal story told by a guy who's visited the site for decades, only to have a perfect 6" C. megalodon tooth be found by a kid after only a few minutes of searching. This post deals with various marine mammal related "folklore" I've heard, and hope to set the record straight.

No, you don't have a Prosqualodon tooth

This first myth applies principally to North America, and didn't really bother me until I had spent a few years in the field of marine mammal paleontology. Fossil collectors in the US often refer to large odontocete (toothed whale) teeth that do not match Squalodon (see below) as Prosqualodon. Most of these teeth look nothing like Squalodon - they are single rooted, with a greatly inflated root, and a small conical crown. I guarantee that if you search "Prosqualodon tooth" on google you will see dozens of these for sale. One site goes so far as to call these "Prosqualodon errabundus", which is extra hilarious - and I'll explain why shortly. It seems as though the thought process follows a simple pattern like this: if an odontocete tooth is small, then it is a "porpoise" (see below as well) or "dolphin" and no further attempt at identification is made. If it is a very large tooth with an inflated root and a small crown (or completely worn away crown), then it is a sperm whale. If the tooth is large but double rooted, triangular, and cuspate, then it is Squalodon. And lastly, if the tooth is Squalodon-sized but single rooted with a small conical crown and an inflated root but too small to be a "sperm whale", then it is Prosqualodon. This identification process is obviously oversimplified, but there's a bigger and even more glaringly obvious problem here: Prosqualodon has never been reported in North America.

A large odontocete tooth with a thickened neck of cementum from the Sharktooth Hill Bonebed (photo from that are typically identified as "Prosqualodon" or "Prosqualodon errabundus" by collectors and fossil dealers.

Several species of Prosqualodon have been reported, but all from the southern hemisphere. The type species is Prosqualodon australis, described in the late 19th century and now known from several skulls from the lower Miocene of Patagonia - and morphology is consistent with this taxon being a short-snouted squalodontid. Later in the 20th century, three species were named from Australia and New Zealand. Prosqualodon davidis was described from the lower Miocene of Tasmania, and is arguably the best known of all the four species - with a nearly complete dentition, complete skull, partial mandibles, vertebrae, and an articulated flipper. Unfortunately, the skull is lost but it was figured beautifully by Flynn (1948). Prosqualodon davidis is very similar (also short-snouted), and clearly closely related to P. australis. Prosqualodon marplesi has had a rocky taxonomic history - originally reported by Professor Benham (former zoology chair at my doctoral alma mater, U. Otago), who was a bit arrogant yet committed various taxonomic gaffes during his career. Prosqualodon marplesi was based on an incomplete skull, but transferred to the genus Notocetus within the Squalodelphinidae by Fordyce (1994) based on dental and braincase features as well as cladistic results, and then reassigned to the new genus Otekaikea and placed within the Waipatiidae by Tanaka and Fordyce (2014). The very last species, Prosqualodon hamiltoni, is likely a squalodontid (Fordyce, 1994) but probably a long-snouted form and the skull is not particularly similar to Prosqualodon australis or P. davidis (Fordyce, 1991). Regardless of these New Zealand species being removed from Prosqualodon, something close to Prosqualodon davidis is recorded from the lower Miocene Mt. Harris Formation of New Zealand (Fordyce and Roberts, 2009) but has yet to be described. The only other reported occurrence of Prosqualodon is a couple of vertebrae from the lower Miocene of Venezuela (Sanchez-Villagra et al., 2000) - perhaps not such a reliable occurrence, but technically the only one from the Northern Hemisphere.

The skull and teeth of Prosqualodon davidis from the earliest Miocene of Tasmania. Note the lack of cementum and the complex crown with rugose enamel and accessory cusps - nothing like the North American specimens. From Flynn (1948).

The skull of the dolphin formerly known as Prosqualodon - now Otekaikea.  
From Tanaka and Fordyce (2014).

No fossils of true Prosqualodon have been reported from North America, nor have I seen any unpublished specimens in museum or private collections. Further to the point - why aren't these fossils widely called "Prosqualodon" by US collectors actually Prosqualodon? Prosqualodon davidis has teeth that are similar in most respects to other squalodontids - conical anterior teeth with fluted enamel and double rooted cheek teeth with accessory cusps and finely rugose enamel. Teeth of "Prosqualodon" from the US have nothing in common with true Prosqualodon other than having enamel and a root. So, if not Prosqualodon, then what are they? Could they be "Prosqualodon errabundus" as some commercial fossil dealers call them?

"Squalodon" errabundus was originally reported by Kellogg (1931) off of a single periotic (inner ear bone) from the Sharktooth Hill Bonebed of California. Kellogg considered the periotic to be broken and similar to Squalodon, but it would not be until the last few years that the true affinities of "Squalodon" errabundus would be uncovered. More complete material indicates that "Squalodon" errabundus is actually a strange long snouted "platanistoid" dolphin in the extinct family Allodelphinidae, currently known only from the early and middle Miocene of California, Oregon, Washington, and Japan. I've seen references to "Prosqualodon errabundus" for over a decade, though this binomial combination has never ever been proposed once in the literature - and the idea that this species is not a squalodontid has been kicking around since the mid 1970s, though only formally transferred to Allodelphinidae recently. In 2009, "Squalodon" errabundus was given a new genus and is now Zarhinocetus - seven years ago now, and yet you can still find teeth for sale as "Prosqualodon errabundus". The fact that the species has had its own genus now for almost a decade makes the "Prosqualodon" issue even more humorous.

The skull of Zarhinocetus errabundus from the Sharktooth Hill Bonebed - note the tiny tooth sockets. From Kimura and Barnes (2016).

Which brings us full-circle back to "Prosqualodon" fossils from the US. Could they be Zarhinocetus errabundus? First of all, many "Prosqualodon" teeth are reported from the east coast, and allodelphinids are unknown outside the Pacific. We don't actually know what the teeth of Zarhinocetus errabundus look like, because a tooth has never been found in a jaw or skull condifently identified as Z. errabundus. However, amusingly enough, the tooth sockets of Zarhinocetus are tiny and much too small to house the large teeth commonly identified as "Prosqualodon", and the teeth of closely related Allodelphis and Ninjadelphis are tiny needle-like teeth only 1.5 mm wide at the base. Truth be told, the distinctive specimens from Sharktooth Hill belong to a completely unidentified odontocete with extensive cementum deposits on the roots, leading to enormous inflated roots that dwarf the crown. Aside from this, these teeth are reminiscent of delphinoid teeth - and in my opinion, are similar to teeth of the giant kentriodontid dolphin Hadrodelphis calvertensis from the Calvert Formation of Maryland. They are all single rooted, but decidedly more massive; based on giant earbones I've seen, a giant kentriodontid dolphin is lurking in the Sharktooth Hill Bonebed, waiting to be described - and may be the "owner" of these teeth. In summary, identifications of fossil teeth should be based on anatomical comparisons and not hearsay - which is arguably a failure of professional paleontologists not interfacing enough with the amateur community to set some of these things straight.

A maxilla fragment with teeth (figured upside down as it was originally misidentified as a mandible) of Squalodon sp. from the Miocene of New Jersey. Specimens of true Squalodon from the Atlantic Coastal Plain are restricted to Miocene rocks.  Image from

Not Squalodon: Waipatia hectori, Waipatiidae, Oligocene, New Zealand; very similar teeth are found in the Charleston area. From Tanaka and Fordyce (2015).

Also not Squalodon: Echovenator sandersi, Oligocene, Charleston, South Carolina. From Churchill et al., (2016).

Do you really have a Squalodon tooth?

Odds are, unless you're collecting in the Calvert Formation in Maryland/Virginia or the Pungo River Limestone in North Carolina (as far as North America is concerned anyway), you have probably not found a Squalodon tooth. Why do I say this? All bona fide records of Squalodon in the USA come from those two rock units. There are a couple of random records from New Jersey (e.g. the Squalodon atlanticus holotype). South Carolina, despite popular belief to the contrary, does not have any actual specimens of Squalodon that are verifiable. There is Eosqualodon (formerly identified only as Genus X) from the Oligocene Chandler Bridge Formation, which is similar in size to the smaller Calvert species Squalodon calvertensis, but has teeth that are somewhat more denticulate.
So why identify something as Squalodon? What makes Squalodon? In my own experience collectors assume that any cetacean tooth that resembles a tiny archaeocete tooth with double-roots and accessory cusps is Squalodon. True, Squalodon is one of the last truly heterodont odontocetes - heterodonty is the primitive condition where cheek teeth and incisors look very different. But is Squalodon the only heterodont odontocete? As it turns out, nearly every group of dolphins in the Oligocene were heterodont - including agorophiids (common in the Oligocene of South Carolina), simocetids (possibly present), waipatiids (also common), and xenorophids (perhaps the most common odontocetes). There's even a Squalodon-like giant dolphin known currently only as "Genus Y" that has heterodont teeth, but may not be closely related to squalodontids at all.
Collectors in the Charleston area should, for the time being, stop identifying local specimens as Squalodon, since I've not seen any from this area that can be identified as Squalodon - we only have one real South Carolina Squalodon specimen in our collections at CCNHM, but it's a tooth found down in Beaufort County where there are Miocene rocks exposed.

Carcharodon hastalis teeth found in association with a skeleton of the Miocene baleen whale Incakujira from Peru (Yuji, 2014).

I found this shark tooth near this whale bone – the shark must have eaten it!”

This is a very common misconception. Whale bones are often found with shark tooth bite marks – a skeleton recently donated to us has bite marks on more than 30% of the skelton, and relative to the paltry number of such traces I recorded in the Purisima Formation assemblage, the number of shark-bitten bones on the east coast is staggering. Such traces are god evidence of fossil behavior – and different traces reflecting different types of teeth have been named as trace fossils (ichnofossils). However, the case is more difficult to make when there are no such traces. Slow deposition can result in a slightly higher than normal concentration of teeth in addition to marine mammal bones. Association of bones and teeth – especially if the “skeleton” consists of just a couple of bones or a single bone – are commonly formed by sedimentary reworking and concentration. If any sign of transport or reworking is obvious – abrasion, polish, fragmentation – then the fossil association is almost certainly caused by reworking. If the fossils were found in a bonebed, then it's not possible to infer any behavior. The following conditions must be met to infer predation-based association of shark teeth and a prey item in the marine vertebrate fossil record: 1) there must be evidence that the prey animal (marine mammal in our case) represents a single individual and is isolated in the sediment; 2) there must not be any evidence that the associated teeth are from a condensed section, during which vertical differences may not indicate closeness in time; 3) the shark teeth must be found near the skeleton and in a higher concentration than surrounding sediment. Classic bulletproof examples include articulated marine mammals and marine reptiles preserved in fine-grained deposits with dozens to hundreds of shark teeth clustered in a halo around the skeleton. In extremely rare cases shark teeth may even be embedded into bone - clear evidence of predation activity.

Some baleen whale vertebrae with unfused vertebral epiphyses - Miocene Calvert Formation, Carmel Church Quarry, Virgina. Image from

There are a lot of unfused vertebrae here – so this was a whale calving ground.”

Isolated cetacean vertebrae are informally considered some of the most boring fossils from Miocene and Pliocene rocks. Whales and dolphins have high vertebral count, and owing to the loss of hindlimbs, whale and dolphin skeletons are ¾ ribs and vertebrae by count. Fusion of epiphyseal plates – whether in vertebrae, or limb bones – is a hallmark feature of mammalian growth. These are the so-called “growth plates” that doctors will evaluate growth/cessation of growth in young teens based on X-rays. Several basins, including the Chesapeake embayment (e.g. Calvert Cliffs) and the Charleston embayment (Oligocene Ashley/Chandler Bridge formations) have been formally and informally identified as “calving grounds” owing to the high number of cetacean vertebrae with unfused epiphyses. However, studies of modern cetacean epiphyseal demonstrate that not all vertebrae in the column fuse in every species, and it does not necessarily correspond to maturity. Furthermore, epiphyseal fusion occurs when cetaceans (like other mammals) occurs relatively close to skeletal maturity – so cetaceans will have unfused vertebrae for a period of several years. This means that individuals significantly older than neonates (calves) will possess unfused vertebrae, and thus the presence of abundant unfused vertebrae in a particular area has no bearing on age as it could signify somewhat older individuals that have already undertaken migrations (and may have been calved/born in a completely different region). Some species retain unfused vertebrae longer than others, so there is a taxonomic complication as well.

Conical teeth in a dolphin (Delphinidae, left) and spatulate teeth in a porpoise (Phocoenidae, right). Image from www.

"This tooth is from a dolphin and this one is from a porpoise."

This is a common one. Truth be told, when fossil collectors tell me a particular tooth is from a dolphin v. a porpoise, I have no idea what (if any) criteria is used. The terms dolphin and porpoise have changed in meaning through time, and formerly were actually synonyms. Many delphinid dolphins as recently as the 1970s were referred to as porpoises. The current meaning refers to the Phocoenidae – a half dozen species of small bodied, short-snouted delphinoids typically found in temperate to subpolar coastal environments around the globe. All modern phocoenids share spatulate teeth – they almost resemble the tooth of an ankylosaur if all the little cusps were eroded. The crowns of the teeth are shaped like little spatulas or shovels, whereas the teeth of oceanic dolphins (Delphinidae) are almost entirely conical (which is primitive for most odontocete groups). True spatulate teeth representing phocoenids are very rare in the rock record – most of them are from the North Pacific and the west coast of South America, dating back only 10-12 million years (possibly older in Japan, judging from some fascinating research presented last year at SVP). The Atlantic coastal plain has zero published records of fossil phocoenids, and I have only seen a single spatulate tooth from the east coast – currently in a private collection, and if I recall correctly, from the Peace River in Florida (Plio-Pleistocene). There are a couple of phocoenid species from Pliocene deposits in Belgium, suggesting that we should find them in the western North Atlantic Pliocene – but evidence so far has not been forthcoming. Further complicating matters is that many extinct phocoenid porpoises actually primitively retain conical teeth, indicating that only the most modernized porpoises evolved the characeristic spatulate teeth. Many archaic phocoenids from the Pacific retain asymmetrical delphinid-like skulls, blurring the lines between the families. So the take home message is this: 1) porpoise has a very specific meaning (Phocoenidae) and 2) true porpoises (Phocoenidae) are currently known reputably from fossil sites along the margins of the Pacific and North Sea only – meaning if you are an east coast fossil collector, you have probably not found a porpoise.

L. G. Barnes and R. E. Reynolds. 2009. A new species of early Miocene allodelphinid dolphin (Cetacea, Odontoceti, Platanistoidea) from Cajon Pass, Southern California, U.S.A. Museum of Northern Arizona Bulletin 65:483-507

W. B. Benham. 1937. The skull and other parts of the skeleton of Prosqualodon hamiltoni. Transactions of the Royal Society of New Zealand 67(1):8-14

M. Churchill, M. Martinez-Cáceres, C. Muizon, J. Mnieckowski, and J. H. Geisler. 2016. The Origin of High-Frequency Hearing in Whales. Current Biology 26:1-6

T. T. Flynn. 1948. Description of Prosqualodon davidi Flynn, a fossil cetacean from Tasmania. Transactions of the Zoological Society of London 26:153-195

R. E. Fordyce. 1991. A new look at the fossil vertebrate record of New Zealand. Vertebrate Palaeontology of Australasia 1191-1316

R. E. Fordyce. 1994. Waipatia maerewhenua, New Genus and New Species, Waipatiidae, New Family, an archaic late Oligocene dolphin (Cetacea: Odontoceti: Platanistoidea) from New Zealand. Contributions in Marine Mammal Paleontology Honoring Frank C. Whitmore Jr., Proceedings of the San Diego Society of Natural History 29:147-176

R. E. Fordyce and C. D. Roberts. 2009. Fossil Pinnipedia and Cetacea. In D. P. Gordon (ed.), New Zealand Inventory of Biodiversity 553

M. D. Gottfried, D. J. Bohaska, and F. C. Whitmore, Jr. 1994. Miocene cetaceans of the Chesapeake Group. Proceedings of the San Diego Society of Natural History 29:229-238

R. Kellogg. 1931. Pelagic mammals of the Temblor Formation of the Kern River region, California. Proceedings of the California Academy of Science 19(12):217-397

T. Kimura and L. G. Barnes. 2016. New Miocene fossil Allodelphinidae (Cetacea, Odontoceti, Platanistoidea) from the North Pacific Ocean. Bulletin of the Gunma Museum of Natural History 20:1-58

R.W. Purdy. 1996. Paleoecology of white sharks; pp. 67-78 in A. P. Klimley and D. G. Ainley (eds.), Great White Sharks: The Biology of Carcharodon carcharias. Academic Press, San Diego, California.

M. R. Sanchez-Villagra, R. J. Burnham, D.C. Campbell, R.M. Feldmann, E.S. Gaffney, R.S. Kay, R. Lozsan, R. Purdy, and J.G.M. Thewissen. 2000. A new near-shore marine fauna and flora from the early Neogene of northwestern Venezuela. Journal of Paleontology 74(5):957-968

T. Yuji. 2014. A dense occurrence of teeth of fossil "mako" shark ("Isurus" hastalis: Chondrichthyes, Lamniformes) associated with a balaenopterid-whale skeleton of the late Miocene Pisco Formation, Peru, South America. Bulletin of the Gunma Museum of Natural History 187:77-86.

Y. Tanaka and R. E. Fordyce. 2014. Fossil dolphin Otekaikea marplesi (Latest Oligocene, New Zealand) expands the morphological and taxonomic diversity of Oligocene cetaceans. PLoS One 9(9):e107972

Tuesday, September 13, 2016

Paleontological research tips IV: the art and science of maintaining a research notebook

Other posts in this series:

Paleontological Research Tips I: field notes for amateurs and professionals alike

Paleontological Research Tips II: field notes, continued 

Paleontological Research Tips III: a complete idiot's guide to taking decent specimen photographs

Paleontological Research Tips V: manuscript writing, research productivity, peer review, and more

I’ve taken half a year off from blog writing, ostensibly to catch up on manuscript writing. It’s been somewhat useful, but now it’s gotten to the point where I just feel bad. So, Paleo research tips returns to Coastal Paleo. I hope to keep this up at a more regular pace than before. This post is likely to be useful to anyone conducting exploratory natural history research – but may be less useful to those whose research consists entirely of statistics (though, read to the end). 

Continuing the “underpants gnomes” joke from south park, we’re sort of at this stage:

Step 1: fossils
Step 2: get data
Step 3:???
Step 4: paper (profit)

This blog post gives some more subjective tips on what to do after you’ve recorded data/field notes and how to organize that information using actual pen and paper and distill it down into a coherent story you can type up into a manuscript.

All of my research notebooks - two notebooks dedicated to eomysticetids from my Ph.D. (look for New Zealand beer labels), an entire notebook just on Herpetocetus (Blue Moon label), and an entire notebook on marine vertebrate taphonomy.

Why bother with an actual notebook?

For some of my readers, there is no doubt that this post may sound like it was written by a Luddite. We’ve got computers, tablets, iphones, apple watches, and refrigerators with twitter installed on them (I’m seriouslynot kidding, and I really, really wish I was) – so why should we bother with keeping a physical notebook for research? Why not just keep everything as MS word documents on your computer, or in cloud storage?

There are a number of reasons for/against, and I’m not going to pass judgement on one side or the other; both sides – traditional notekeeping, and digital notekeeping – have compelling arguments to be made, and so it largely boils down to picking options based on personal preference and the sort of science you’re doing. Recent cloud storage hacks raise the possibility of losing data. Hard disk drives are not permanent, and generally last about seven years. I almost lost ten years of data, unwritten manuscripts, and digital photographs when my hard drive died this summer, and as my hard disk was slowly dying, I realized I did not have enough money to pay for a new one. Eventually I saved up some over the summer and picked up a new one, meanwhile adding a solid-state drive and an upgraded power supply, and I got very, very lucky. I’ve gone through a dozen flash drives over the past decade, with various drives either getting corrupted somehow or being lost. Requiring a device to work on research can be impractical at times: you very likely will run into a situation where a dank museum basement may not have an appropriately placed plug, let alone a wireless (or wired) internet connection. Digital research notes have their upsides – you can instantly share information with coauthors. There are also digital calipers out there which can be set up so that measurements are automatically entered into a spreadsheet. Large spreadsheets are much, much easier to work with electronically than rather than on a sheet of paper; recording many sorts of data are easier to do digitally. Notebooks can also get a bit heavy; I’ve filled up over half a dozen moleskine notebooks since I started using them eight years ago, and I need to remember to grab the correct one with me – this is obviously not a problem with a laptop or a tablet. Lastly, at some point, we are no longer sending handwritten manuscripts (or even typewritten, for that matter) in to journals, and we’re all using MS word or a similar program to write the end-result of our research with – so why not go digital all the way?

But what about “real” notebooks that aren’t written in binary? For starters, time and again I see in the news new studies being published indicating that notes written by hand being stored more firmly in your memory. Full disclosure: I’ve not bothered to read any of these studies first hand, mind you, but since they reinforce my own biases and personal experience they sound eminently plausible. I personally have a much easier time recalling information I’ve written out by hand. Colleagues, friends, and my dear wife routinely make fun of me for my abnormally sharp memory for unimportant things like fossils (my brain is a library of fossils and their morphology & locality details) and Star Wars, and yet in school I could never remember when my damn homework was due. Point is, if memory is an issue for someone like me who can recall the date, time, and location of a particular fossil I collected six years ago down to one meter – then likely it is an important issue for everyone.

Actual notebooks don’t run on electricity, and don’t take a minute to boot up. They also don’t have annoying pop-up windows telling you that your free McAfee antivirus trial ended 11 months ago (no, I’m not going to give you any money for something that works half as well as freeware, now piss off McAfee!). I’ve never heard of a notebook breaking if you dropped it. Notebooks also won’t become corrupted, or crash, if used improperly or left on the shelf for too long.But just like electronics, notebooks have their limitations. Both will be lost permanently in a house fire or natural disaster; both will be completely screwed if you spill enough coffee on them (as I type this, I nervously push my coffee mug further away). Both will be ruined if your checked bag busts open on the tarmac at SEATAC; of course it’s raining, it’s Seattle (this did happen to me, but ironically it was a checked box with part of a fossil whale skull inside; the box was damaged but the whale was in a concretion, so it was fine). As a result of these very real fears, whenever I travel my top priority is to have ALL notebooks I’m traveling with inside my carry-ons. On my way back from New Zealand, this meant I had ~15 field and “lab” notebooks in my two carry-on bags, which was a bit ridiculous.
Another issue is that of “language”. Storing certain information digitally has long term problems, and the most prominent problem I’m thinking of starts and ends with file extension. Try opening certain file extensions in MS Word 2010 – sometimes it’s impossible. Sure, Microsoft puts out file compatability packs, but what about when we’re on MS Word 2015, and they decide to stop supporting software/file types that are older than 10 years? I hate MS Word 2007 & 2010, and still use Word 2003 whenever possible as it is by far the most intuitive to me. My dad is an attorney and has used Word Perfect since the 1980s, and until the last five years it was the typical word processor of choice for those in law. The version of Word Perfect he uses is now 15 years old, and he has to run a Windows XP emulator in order to even run the software – he dislikes the newer version, paralleling my frustration with Word 2007/2010. This is not just a matter of poor choices – many of his older legal files are accessible only using Word Perfect and not through Word, and attorneys are required to save all documentation for a long period of time (10 years, I believe). 

Likewise, this problem of having the information but being helpless to actually read it is not unique to electronics and software that are constantly being updated and tweaked, often at the expense of existing products. Notes must be written neatly enough and in a comprehensible language in order to be useful. I used to have terrible handwriting, and I realized when I was a Freshmen in college that I could no longer write in lower case, and began writing in all-caps with a sort of easy-to-read block printing. I can open up notebooks from my master’s program and still read everything. I can’t say the same for class notes from high school, written in incomprehensible chicken-scratch. Can I read anything in cursive? Only if it’s immaculate. I was probably one of the last cohorts of students to be taught how to write in cursive; I stopped using it as soon as I was no longer being graded on it, and so my skills are very rudimentary, frozen in time from third grade. During my Ph.D., Morgan Churchill and I started researching a fragmentary fossil called the Waipunga seal (our eventual research was just published in NZJGG). When we took the specimen on loan from GNS in Wellington, we were generously sent along Dr. J.A. Berry’s (Napier, NZ) notes on the fossil. I was excited to see them – a time capsule of thoughts on a completely overlooked fossil from the early 20th century, when many “modern” ideas of pinniped relationships we take for granted did not exist. Morgan and I opened up the folder and were disappointed to see an inch thick stack of loose sheets of paper with messy, cursive-esque squiggles – the notes were completely useless, probably readable only to Dr. Berry. I could make out perhaps one or two individual words on every two or three sheets. 20th century pinnipedologist Dr. Judith King published on several other specimens Berry worked on, and remarked in each case that Dr. Berry deserved credit for his correct identifications, but that his manuscripts were not in a state to be published; I doubt that Dr. King had much more luck deciphering Dr. Berry’s cuneiform than I had, and I assume that she was being nicer about it than I am currently.

Utterly gorgeous entry from one Leonardo Da Vinci's notes, one of the most famous pages of any scientific notebook in history.

A more famous example, of course, is Leonardo Da Vinci, who wrote backwards – and many believe this was done to keep others from reading his notes. However, I’ve also seen others note that he was left handed and did this to keep ink from smudging. If you want your data to outlive you, please don’t turn your notebook into the Voynich Manuscript

Other reasons exist for using real notebooks. It’s much, much easier to include sketches interspersed with handwritten notes, for example, and I’ll wager that most people can produce a sketch (or reproduce one, if in class) much faster with pen and paper than with mouse (or a touch screen for that matter). Sure, the software does exist for quickly adding sketches into text, but it comes across to me as less convenient. There is certainly an aesthetic element to it as well – it feels damn good to look through old notes when working on research, seeing carefully written text associated with annotated photographs and sketches, cross-referenced to other sections in the notebook (and indeed, other notebooks) – having a well-organized notebook can be a thing of beauty. This may seem shallow and superficial, and there are certainly sci-hipsters out there who will get all uppity about notebook brands (moleskines are expensive, moreso than when I started – perhaps thanks to hipster assholes – but I am anal retentive enough that I want all of my notebooks to match one another). However, keeping a properly organized notebook is the best way I know of to organize and consolidate all of my thoughts on a particular research subject, and permit me to convert disconnected observations into a cohesive story and help me feel like an organized person (which is now a 31 year-long effort that is finally succeeding). If you can get this same feeling from digital note-taking, great! I don’t know how you do it, and if that accurately describes you, then you can stop reading here. Lastly, and perhaps most fundamentally, I dislike staring at computer screens for too long and I get distracted easily – I also am very susceptible to headaches, and suffer from them almost daily. Bright screens trigger headaches after a couple of hours (and on that note, it’s time to go take a break and check on our 3D printer and fossils sitting in acid baths). Writing in notebooks solves all of the above problems (which are NOT universal!) and for me, and surely many others, mark a critical stage in the condensation of ideas between the nebulous conditions in the brain and the refined format of a manuscript and resulting journal article.

What sort of notebook?

This section is by far and away the most subjective, and owing to that I’ll keep it short. There are some heinously expensive notebooks out there – I use Moleskine notebooks, which are moderately priced, and have increased in price by ~30% since I bought my first in 2008. They come in a number of sizes, have nice college-ruled lines, a decent page thickness that keeps ink from bleeding through, and come with a page-marker ribbon and a pocket on the back cover for scraps. I keep printed photos in here if I’m working on a large project and have a lot of photos to paste in. If you don’t want to spend 20$ on a 10x7.5” notebook, there are plenty of knock-offs at half the price that are probably of similar quality. Some colleagues of mine just use those funny composition notebooks with the speckled black/white covers; my undergraduate adviser, Dr. Dave Varricchio, had a single monograph written out in four of these notebooks. I started with hardcover, smaller moleskines, and within a few years was a bit tired of the small format and upgraded to somewhat larger and more expensive notebooks. Moleskine does make much, much larger notebooks (like 12x20” or so) but these were 50$ when I saw them in New Zealand (although, that’s just how much any book costs down under). As far as what sort of notebook to pick, you should weigh 1) line ruling 2) paper thickness (if you use ink that bleeds, a lot of your notes will be unreadable), 3) notebook size (larger notebooks can fit larger diagrams & annotated photos; my handwriting is also messier in smaller notebooks), and of course 4) your budget. Most scientists are academics of course, used to living off of bread crumbs. My view was that a 20$ purchase would give me more than a year’s worth of notes; indeed, I have perhaps spent only 100$ on notebooks over the past 8 years. Most techies would surely drop several times that amount at the slightest announcement of the newest Iphone (It’s got headphones without a cable! You’ll feel better than everyone!).

Table of contents from my first notebook on cetaceans; most of this has all been published by now.

Where to start? Basic organization

At the very beginning of course, it’s a very good place to start. In all seriousness, the first page should include some brief description of what will go into the notebook, if for example you’re like me and have different notebooks for different topics. Name, affiliation, contact information, and a reward in dollar amount in case it goes missing. My guess is that a thief or good Samaritan are more likely to swipe an Ipad over a research notebook filled with labeled pictures of bones. 100$ is a good bet for a reward, in my opinion, though that’s entirely a guess as I’ve never had to worry about that problem.
Next up should be a table of contents. I block off the first few pages for the TOC to give room for expansion – a typical entry will be 5-15 pages in length. If you anticipate your entries to be longer, you can always subdivide it and include those subdivisions into the TOC – or just allot fewer pages for the TOC. My TOC has “subject” on the left and “page #s” on the right, and I even use little dots like in an actual TOC/index in a book. Whenever I start a new entry, I’ll add it into the TOC and indicate the starting page, leaving room of course for the last page. And that means numbering every single damn page in the notebook; you don’t need to do it all in one go – I add in page numbers as I write.

With each entry, I try to include the full title on the first page, and on subsequent pages simply write a shortened title followed by “cntd.” There will come a time when you will have to abandon an entry, begin a new entry, and return to the former subject and therefore split an entry; on the last page, I write “continued on page…” and fill in the page number when I get back to it. This requires diligent revisiting of older sections on occasion. For a split section, I tend to also add that in as a separate TOC entry – e.g. “Description of a Cambrian rabbit fossil part 1…….p. 84-96; Description of a Cambrian rabbit part 2…….p.109-121.”

Occasionally I might have multiple notebooks where I might refer to an observation I have made that is not yet published – in which case I will reference the notebook title (I also number all of my notebooks in roman numerals, I-VIII at present) and page number. This also works if you need to refer to field notes. When appropriate, I will often completely copy field note entries for a particular fossil description entry. It may also be important to note the date each entry was – in case, for example, a museum visit opens your eyes to some new pattern and you have to reevaluate all of your assumptions and biases regarding some aspect of the fossil record (such as my 2013 visit to the Cooper Center in Orange County did about fossil pinnipeds).

Labeled fold-out photograph of the holotype skull of the eomysticetid whale Tokarahia kauaeroa.

Including illustrations and photographs

This is where you can get a bit creative, and can blur the lines between science and scrapbooking. Paleontology and many other branches of natural history research are visual, and there’s no better way to make your work accessible to your future self than supplementing written notes with hand-drawn sketches/diagrams or photographs. My undergrad adviser Dave Varricchio would take photos in the field with a Polaroid camera, shake the picture, and tape it directly into his field notebook – carefully annotating the position of individual bones and sedimentary contacts/bedding and burrows as he excavated a site (this is precisely how Dave painstakingly documented the den of the first burrowing dinosaur, Oryctodromeus cubicularis). I remember helping out at a marine crocodile excavation in the Thermopolis Shale in 2009 as Dave took his last few polaroid shots – the company had just stopped producing the film, and he ran out (I believe they make the film again now, though). I took that idea and ran with it – it’s not quite as efficient, but if I know I’ll be writing about a particular fossil, I’ll snap some digital photos, quickly edit them in photoshop, and arrange them into a single image and print them off on a laser printer. I used to print everything off on photo paper, but I found that A) photo paper is heavy and thick and B) the ink rubs off after only a few months of notebook use. My laser printer images, however, are all still sharp 5-6 years later. I annotate these using a different colored pen (red for annotations, black/blue for the main text). I treat these as the proto-figures for a project – often by the time I am done with the entry, I’ve figured out what works and what doesn’t and edit the final images accordingly. If a specimen or other image is too big for a single sheet, I fold them in half and glue (old fashioned glue sticks work well) one side down – and now you’ve got a cute flip-out image that is appropriately sized. Any images that will help you consolidate your thoughts can be included – I tend to include maps, labeled anatomical & comparative photographs, and when relevant even graphs.

An example of photo paper beginning to smudge after years of use - the notes (circa 2008) from my very first research project on the fur seal Callorhinus, published in JVP in 2011.

If you are artistically inclined, sketching directly into the notebook is a great way to supplement your text. If you find yourself in a descriptive field within natural history, sketching is an eminently useful skill – it improves your powers of observation and attention to detail. If art is not your strong suit, I recommend setting aside some time and learning – practice makes perfect, and artistic talent is a myth. “Talent” is nothing other than investing time into artwork and practicing regardless of how many crappy drawings you produce at first. My art used to be terrible, and it wasn’t until High School when I took four years of drawing classes; that much practice will turn anybody into a serious artist. Many people I’ve met believe that art is quickly done – and it can be, given the medium – but more often than not those wishing for instant gratification will lose interest or become discouraged when they do not get instant results. I recommend those people take up photography instead (and then, why not re-read Paleo Research Tips Part III: fossil photography?). In all seriousness, at the very least I recommend taking up art as a hobby to keep yourself sane during graduate school; I taught myself watercolor so I wouldn’t go insane during my Ph.D., and taught myself acrylic on canvas when I got my first job and could afford the supplies, as well as being a rite of passage as an “adult/grown-up” artist).

Notes from my taphonomic literature review from my master's thesis; depicted here are notes on phosphogenesis and Osedax bioerosion.

Literature review

Maintaining a research notebook may not completely revolve around primary research at first. When I started my master’s thesis on marine vertebrate taphonomy, I quickly realized that I had a firm grasp of most of the available literature (hint: there’s not much) and that having a solid grasp on all of the relevant literature was within arm’s reach. Aside from reading, I was unsure how to proceed. Type up bullet points? Again, I found that such activity did little to maintain mental permanence. Then I thought, why don’t I buy another moleskine and write notes on each paper I read? I started another notebook and recorded notes on most of the relevant papers on marine vertebrate taphonomy. Certain ideas are best communicated through diagrams, graphs, and photographs – so I photocopied the most important figures from each paper and pasted them into the notebook. In each entry, I distilled each paper into a series of bullet points – and in some cases, I noted where certain papers on whale taphonomy were simply reinventing the wheel and making a big deal out of recycled ideas from 20-30 years ago. “Calling bullshit” is an important part of the literature review process, after all. Six years later and most of these papers and the most relevant bullet points are still somewhat fresh in my memory – and if not, I can go back to my distilled notes and save myself the trouble of doing it all over again. This sounds quite a bit like revisiting notes from college courses [confession time: I did not bother keeping many of my notes from college; so long as it pertained to sedimentary geology or paleontology, the act of writing it down and re-reading it once or twice prior to exams has burned most of it into my uncanny memory].

Labeled tabs (up to date for most of these) allow easy and quick location of relevant entries.

Miscellaneous Tips

-To keep super organized, I add in little colored plastic tabs and write (with a fine point micron pen) for each entry. I can quickly refer to that topic when necessary.

-This might be my anal retention showing, but I tend to edit photographs prior to pasting them into notebooks because I strongly dislike including photographs with the background left in. It introduces a bit of extra work, particularly if you’re using “working photographs” (as they’re called in the Fordyce Lab) which will not be used in the final publication, meaning that two rounds of photo editing are needed. This also, however, means that you can do a faster, sloppier editing job if it’s just going into your notebook.

-The utility of this sort of activity is not relegated to primarily descriptive work. When interpreting graphs and charts of taphonomic data, I’ve found that being able to lay out all possible interpretations and relevant observations within a notebook permits me to pick and choose the more relevant points to include in the eventual paper.

-Not really a tip, but more of an observation that is better shoehorned in here than elsewhere in the post: I find that when I’m done writing an entry in one of my notebooks, the manuscript is already 75% written, and can be typed up directly from the notebook.

-I've included a few tips for embellishing notebooks. There's an entire webpage dedicated to modifying moleskine notebooks. Check out the "Moleskine hacks archive".

-Have other tips for maintaining research notes in a traditional manner? Let me know, and I’m more than happy to include it here!

This entry in the paleontological research tips series is admittedly quite a bit more open-ended than the field notes section. After all, there are many more guidelines about what should be written in the field, given that in some cases field notes belonging to certain geologists may be subpoenaed for legal purposes. For field paleontology, there are some very black and white rules as to what information needs to be recorded. As far as research in the laboratory or museum goes, it is admittedly much more subjective and revolves around what works best for individual researchers; I’ve outlined my own methodology in the hopes that it might give ideas or inspiration to students in my position eight years ago – knowing which direction to go with research, but unclear about how to organize thoughts between the “get data" and "profit" stages of research.

Saturday, February 13, 2016

Paleontological Research Tips III: a complete idiot's guide to taking decent specimen photographs

Other posts in this series:

Paleontological Research Tips I: field notes for amateurs and professionals alike

Paleontological Research Tips II: field notes, continued 

Paleontological Research Tips IV: the art and science of maintaining a research notebook

Paleontological Research Tips V: manuscript writing, research productivity, peer review, and more

Here's the third installment of my series on paleontological research tips! This one is on specimen photography. It took me years to learn all this crap, picking up tips here and there from various sources, but the sheer majority of this was learned from my Ph.D. adviser R. Ewan Fordyce who is an unusually talented and skilled photographer. Ewan passes down much of his knowledge to his students, and we try to pick up as much of it as possible. Some paleontologists don't worry enough about taking and publishing good photographs, whereas others worry too much - photography can seem daunting, but it's OK - we're all here to repent and better ourselves through learning.

A very valuable skill to have as a paleontologist - and many scientists in general - is the ability to take high quality photographs that are acceptable for publication. Evidently, judging from the figures of many published papers I've read, I see that there is quite a lot of room for improvement. As per usual I won't name any names, and rather than pretend that I was born perfect and have not learned anything, I'll go ahead and make fun of some of my earlier published figures before I learned what I know about photography now. So, before I go into the nitty gritty, let's look at a couple of figures with several photographs each and critique what we can see.

Here's a shining example of a published figure I'm not very proud of - Boessenecker 2013: J. Paleo.

The two examples here are a figure I'm not so proud of, and another which I find to be one of my most visually satisfying figures. The first figure is from my J. Paleo paper on barnacle encrusted sea lion bones from Oregon, one of my first post-master's degree manuscripts which had a bit of a tortured review history, and I had taken all of the photos in fall of 2011. I started attempting (notice the word choice!) to publish the paper in summer 2012 when I was in NZ (northern, not austral summer) - which meant that I could not re-take the photos. I was beginning to learn at that point, and new that the photos weren't great, but had no idea when I'd be able to go back to UCMP at Berkeley where the fossils were. Even the reviewers complained about the photos. The lighting and contrast is a bit different, with the dorsal views having much higher contrast and being somewhat sharper; part 4 is washed out and mostly out of focus, and the same can be argued for part 3; parts 1 and 2 look fine. In part 5, the transverse processes are out of focus; part 6 is almost entirely in focus, but washed out. These photos were shot hand-held under direct sunlight, hence the 1) fine scale fuzziness and 2) extreme contrast.

And a figure with much, much better lighting, contrast, focus, and detail: the holotype periotic of Tohoraata raekohao. From Boessenecker and Fordyce 2015: Papers in Palaeontology.

The next figure is one I'm much more proud of - the periotic (inner ear bone) of the eomysticetid Tohoraata raekohao, derived from the first chapter of my Ph.D. thesis at University of Otago. This is not the published figure, but rather the super-dense and overly chaotic figure at the time of initial submission. Ignoring the anatomical labels written in the manner of a crazy person's living room wall manifesto, the photos are quite nice. All of them are consistent in lighting, contrast, lighting direction, and clarity. Everything is in focus - which is a bit of an impossibility for some lenses, but there is an advanced method to take care of that which I'll discuss below (see Advanced tips: focus stacking). In general, I can't point out anything glaringly obvious that's bad with this one, and am overall quite pleased. I did, after all, have to get my Ph.D. adviser R. Ewan Fordyce - well known in the field for painstakingly taking incredibly good photographs - to give me the OK to publish these images. These images were shot with 1) ammonium chloride coating, 2) focus-stacking for continuous focus, 3) soft lighting, 4) under manual setting with correct exposure set, and 5) on a camera stand.

My personal photography kit: yes, I bring all this crap with me to every museum visit. It's a pain, but it permits me maximum flexibility. Large camera tripod, medium tripod for LED lamp, tiny tripod, LED lamp, manual shutter release, camera body, short zoom, telephoto zoom lens, and of course a scale bar!

An example of my basic setup: camera tripod, fossil/scale bar on a white background, and the LED lamp positioned at upper left of photo.

Basic tips 1: the camera

I'll get this out of the way at the start: sure, you might be capable of taking decent photographs with a point and shoot or a smartphone, but for the purposes of this post I'm going to be talking about real cameras that have all sorts of scary knobs and dials with numbers on them. I'm talking about DSLR cameras - digital single lens reflex camera. I've met many people who buy these cameras, which often cost 400-500 us$ at the cheapest, and leave the camera setting on auto (the green box on the dial), and taking hundreds of crap photos for every good photo - wondering why they spent so damn much on the camera. You can treat an expensive DSLR like an overpriced point and shoot camera, but it's a bit like buying an armored humvee with a machine gun port on the roof to go grocery shopping and drop the girls off at soccer practice. So, if you want to take pictures with a smartphone or a crappy point and shoot, be my guest - but you won't be able to use many of the tips below, so go away.

Actually, that's not entirely true: smartphones and point and shoot cameras do have their uses, and owing to their smaller pricetag, are ideally suited towards field photography. Landscape photos out in nature (under regular daytime lighting) are easy to take and smartphones give you the option of panoramic panning photos. Because field photos are relatively easy, we're basically going to ignore them and mostly discuss close-up photographs of specimens.

DSLRs are pricey, but essentially anything where you can use a manual setting and change ISO, aperture (aka F-stop), and shutter speed is desirable. On smartphones/point and shoots only automatic settings are generally possible and the camera does it automatically for you. The camera is dumb; don't let it make decisions for you. I've got a relatively basic Canon Rebel EOS, but have used Nikon D1200, D700, and a D90 during my Ph.D. 

Basic tips 2: the lens

I'll admit I'm not that much of an expert on lenses, so this will be brief. Most cameras come with a standard 55-85 mm zoom lens; I've got a decent lens that came with an old film camera that took a swim in Monterey bay during fieldwork, which killed the camera but not the lens - and the lens is still happily clicking away on my current DSLR. Zoom lenses are great: the width of the photo can be modified, as can focus, but generally speaking the image quality is somewhat lower than a fixed focal length AKA prime lens. Prime lenses produce higher quality images, have a wider aperture (more on this below), and are generally lighter in weight as they have fewer internal lenses and working parts. The rub is that the focal length is fixed, meaning that if you are standing X feet away and cannot fit everything into frame, you cannot simply zoom out and either need to back away from the subject or swap with a different lens.

With prime lenses, the lower the number the shorter the lens and the wider the field of view; a standard prime lens is 50 mm, whereas a telephoto is 135mm, and a wide or extra wide angle lens is 34-14 mm (respectively). The shorter the prime lens, the greater the distortion (wide angle and extra wide approach a fish-eye lens), whereas minimal distortion is present in standard, telephoto, or super telephoto lenses. Here's the other rub: prime lenses are expensive, and if taking photos of a sporting event, it can be a pain in the ass to switch lenses. Luckily, fossils are not exactly fast-moving, so if well-funded, that's not really a problem.

Don't have a lot of money? Me neither! Zoom lenses work just fine and I've done a side-by-side comparison of photography using my cheap DSLR with a zoom lens, using the same lighting setup, and switching it out with a Nikon D90 with expensive prime lenses and the results are quite favorable. I still like the results with the expensive camera slightly more, but in general most would be hard-pressed to actually tell the difference. One last note: the limiting factor for taking good photos will be the lens, not the camera body. If you've got an expensive camera body with shit lenses, you will take photos that look crappier than an expensive high quality lens on a shit camera body.

A super handy chart showing what different aperture (f-stop), shutterspeed, and ISO settings mean for photos, put together by Daniel Peters.

 Basic tips 3: exposure

So you've got a DSLR and some kind of lens. Just put it on auto and click away, right? No! Please don't. You've got a state of the art piece of technology in your hands, and it is not that difficult to learn how to use it properly! The most important thing to learn is exposure - how to juggle different settings in order to take a photo that is at optimal exposure. First, when you look into the viewfinder you'll see a little bar with a zero in the middle and tick marks for -2, -1, +1, and +2. Exposure is essentially how much light is coming into the camera; the camera is set so that zero is optimal exposure, +1 or +2 is overexposed (too much light), and -1 or -2 is underexposed (too little light). "Ok great, let's just press a button to make exposure zero". Nope, doesn't work that way. Exposure is a function of three different settings on your camera: aperture, shutter speed, and ISO. All of these work with eachother to make great photos but if used at their extremes can produce shit.

When shooting in manual on a DSLR you can adjust shutter speed (upper left), aperture (upper middle), and ISO (upper right), the three of which should be adjusted to attain correct exposure using the little scale in the middle. Adjusting these three to get to zero, and maintaining quick enough shutterspeed to take a non-blurry photograph, is half the battle in photography. From

Aperture, known colloquially as F-stop, is a measure of how wide the mechanical aperture of the lens is. The lower the number, the wider the aperture - the higher the number, the smaller the aperture. My little zoom lens ranges from f/5.6 at the widest to f/32 at the smallest. At lower aperture, for god knows what reason (this isn't a post on optical science so read elsewhere if curious) the depth of field narrows - this is the band in which everything is in focus. Also, the closer an object is to the camera, generally speaking the depth of field scales so that it is narrower closer to you - hence the difficulty in focusing with your own eyes on objects close to your face. The higher the f-number, the broader the depth of field, and everything tends to be in focus. The flipside is that if you keep everything else constant, a lower f-number (wider aperture) will produce an overexposed image whereas a higher f-number (narrower aperture) will produce an underexposed image - because of the amount of light coming through the aperture (wider aperture = more light). A good strategy is to split the difference: f/16 is what I typically shoot with for small to medium sized specimens as it permits a decent amount of light but also has an intermediate depth of field.

 Which brings us to shutterspeed. This is literally how long the camera shutter is open for, and is fairly intuitive: the slower the shutter speed, the longer the shutter is open, the more light comes through; the faster the shutter speed, the shorter it is open, less light comes through. This compliments F-stop and the two can be used to balance each other: need to shoot at wide aperture? shutterspeed should be higher. Need everything in focus (high F-number/narrow aperture)? shutterspeed should be lower. Here's the best part: the camera (in this case) does all the thinking for you and automatically calculates the ratio for which settings will produce perfect exposure. A little tick mark on the exposure "bar" in the viewfinder will tell you when you've got each setting at an appropriate place - this is called the exposure meter. If you have your F-stop setting where you want it, just move the shutterspeed dial until the tick mark goes right in the middle; it might jump around a little to +/- 0.25 or so, and that's fine. Shutterspeed will be brought up again below on the issue of camera shake.

ISO is a different issue - this is the sensitivity of the digital sensor to light. Let's say you need to take a photo at narrow aperture, but with appropriate shutterspeed, your photos are blurry because you 1) are shooting in some dimly lit mildewy museum basement, 2) either have drank too much or not enough coffee, or 3) need to eat or 4) do not have a tripod. In this case, not enough light is getting in even with a longer shutterspeed, and the long shutter time is letting motion blur from shaking the camera to make the photo blurry. You can increase the light sensitivity of the sensor by increasing ISO. ISO should normally be set low at 100 or 200. For sub-optimal lighting conditions setting it to 400, 600, or 800 can fix most problems, whereas 1600 ISO essentially permits you to take pictures at night. The flipside is that the higher the ISO the more artifacts make it into the picture - all sorts of graininess which looks shit, anomalous blips of color (usually red), and that doesn't really work well for a published picture. For the most part, unless your shooting fossils at night, ISO won't need to go so high as to introduce noticeable artifacts - and even then, raw photos I've taken of the aurora borealis at midnight in Montana can be edited using so that 90% of the artifacts go away. Again, adjusting ISO will be factored into the camera's exposure meter. ISO can generally be left on a fairly low setting if you are shooting with a tripod or camera stand, and is thus mostly relevant towards handheld shooting.

Here's some examples of different photos of a xenorophid dolphin vertebra taken with varying exposure achieved through different means:

Handheld, on auto, with flash, f/5.6, 1/40 second shutterspeed, and ISO at 400. There's no lighting from upper left, there's a bit of shine, and some weird shadows which make editing challenging.

Taken in manual and handheld with exposure set to zero, f/32, 1/4 second shutterspeed, and ISO 1600. Camera shake! Even with ISO set so high the image is still blurry. I initially set the aperture to be tiny to get this effect for educational purposes. Setting a wider aperture (down to f/5.6 on mine) would have permitted a faster shutterspeed.

Underexposure! Taken using tripod, underxposed by approximately 1-2 full "stops" - f/16, 1/8 second shutterspeed, ISO at 100.

Overexposure - f/10, 1 second exposure, ISO 100. This actually doesn't look too horrible.

This image is ideal, and made use of a tripod, f/16, 1/5 second shutterspeed, and ISO at 400. ISO isn't needed to be that high for this shot, but from an earlier session I discovered our second floor vibrates when large vehicles drive by outside, meaning camera shake even when on a tripod!

A very basic lighting setup, here photographing a small xenorophid dolphin skull on a white sheet. LED lamp at upper left, camera in foreground.

Basic tips 4: lighting

From the prior section it should be obvious that the most important aspect of photography is getting the correct amount of light into the camera. There are ways around shitty lighting, but you don't have to accept dim lighting and deal with it - you can always bring your own light. Spotlights can be useful, but the bulbs burn very hot and can explode. A cheaper alternative is LED lamps - little banks of 100s of LEDs which can be battery powered or plug into an outlet. These use far less electricity, do not get hot, and are very very portable. Most come with a little miniature tripod, but can also be mounted on their own full size tripod. I have one of these, but at U. Otago we had three or four to use. Light intensity can also be adjusted.

Convention dictates that lighting should come from the upper left in published photographs, so that shading and shadows are consistently in the same direction. DO NOT think this translates to "let's use a single light source in a dark room - we still need to see the lower right side! Ideally, you could use four light sources, and have all but the upper left turned to lower light intensity, with the upper left set higher - this will give maximum lighting of all features and conform to the standard "upper left" rule. Only have two lamps? Put the second one at the lower right, but at lower intensity. Only have one? Ambient lighting can be used for most of it (think low F-stop, slow shutter speed, higher ISO) with your lamp positioned again at upper right.

If you have access to a camera stand with four lamps, "great" - many camera stands do not allow adjustment of the light intensity, and I find most to just be cumbersome and awkward and thus to most museums I bring two tripods and an LED lamp which is ultimately more flexible. Alternatively, diffusers can be used to dim non-upper right light sources, or to soften light that is too "hard" (see below).

If working with larger specimens, lighting can be very tricky - at U. Otago we used several large size sheets of white styrofoam to reflect light. It's not quite as effective as a mirror, but still has a noticeable effect and you can really get light into all the tough to see spots on a large specimen with minimal lighting and lots of white sheets. Tyvek cloth works as well - anything you can reasonably use that is white and reflects lots of light in the direction you need it.

Most LED lamps can be placed directly onto the flash mount of a DSLR camera.

Another trick, if you need to get a lot of reference shots but they do not 1) need to have a nice background or 2) need to have consistent lighting from upper left: if you have one, take your LED lamp and stick it on the flash mount - voila! You now have a consistent light source that doesn't flood your fossil with shiny highlights. Set F-stop down at its lowest possible number, and there will be a "Program" setting where you can set ISO to the desired level, set F-stop where you want it, and the camera will automatically set shutterspeed. If ISO is high enough and F-stop low enough, the shutterspeed will be fast enough to take hand-held shots with your lamp mounted. I've done this a lot and it works great. I first experimented with this on my colleague Rachel Racicot's face at the La Brea Tar Pits. This method also saves your camera battery - and most LED lamps run on batteries (double A). Mine has its own special rechargeable battery AND works on double As, and I use a set of rechargeable double A batteries so that one the regular battery wears down, I put in the double As and put the other back onto the charger, and then recharge the double As when necessary - allowing nearly continuous photography.

Osedax craters in the holotype skull of Waharoa ruwhenua, photographed with ammonium chloride coating and low angle diffused LED lighting. From Boessenecker and Fordyce 2014: Lethaia.

Need to photograph subtle surface texture such as patches of bryozoans, bite marks, or other traces? Use low angle lighting - i.e. place the light source low on the "horizon" of the surface being photographed.

Lastly, any increase in the amount of light you can achieve will 1) permit you to shoot at higher f-stop (and therefore with a broader depth of field so more will be in focus), shorter shutter speed (reducing camera shake and therefore reducing blurriness), and lower the necessary ISO (reducing the number of ISO-derived artifacts in the image). More light = better conditions for photography.

OK one more point: unless you know how to manually tinker with flash, DO NOT USE FLASH. Flash often makes fossils appear shiny and often negates all the careful tinkering you've done to master the f-stop, shutter speed, and ISO above in basic tips 3.

Basic tips 5: tripods, camera stands, and shutter release
Camera shake is a terrible thing, and unless you know how to set exposure, play around with f-stop and ISO to get a working shutter speed, you will end up with shitty, blurry photos that will drive your colleagues insane. Fortunately, tripods are cheap! Mine cost 35$ at WalMart. Stick your camera on a tripod (remember to never over-tighten the screw) and you can take long exposure shots with ease. If crappy lighting is all that's possible, just dial down the f-number and shutterspeed and you'll be able to achieve a decent exposure - just don't cough, bump the camera, or let a train or 18 wheeler drive by. Do not press the shutter button yourself - even if done carefully with a super heavy duty expensive tripod, the pressure being released by your finger on the button will cause the camera to shake. Use the timer - on my camera it can be set to 2, 5, or 10 seconds. I'm an impatient bastard, and my camera makes a horrid beeping sound during it and I use an old school manual shutter release - a cord with a button on the end. The button can even be depressed halfway for autofocus - how about that! Remote shutter releases also exist, but I find them equally irritating as some of them need to be recalibrated with the camera every 10 minutes and have a battery of their own. Also, the remote can be lost or misplaced. Corded ones are cheaper, run off of the camera's battery, and are stuck right onto the damned camera so it's pretty difficult to lose them. Most of this applies to camera stands as well: stands reduce camera shake, but often (especially during museum visits) you might be stuck with inflexible lighting.

A lightmaster lightbox my lovely wife got me for my birthday - rather than use conventional halogen or tungsten bulbs, this one is LED powered and is less than 1 cm thick. Though I'll be using it for drafting and artwork rather than photography.

Our giant light box at U. Otago - an old drafting lightbox the size of a refrigerator. The glass was not frosted, so we just laid down a bunch of large sheets of tracing paper to give it a more diffuse effect; LED lamps can just be placed directly on top like this.

One of the lumbar vertebrae of OU 22163, a juvenile specimen of the eomysticetid Waharoa ruwhenua, photographed on a lightbox with diffused soft lighting from upper left - original photo (left) and edited image on right as used in Boessenecker and Fordyce 2015: PeerJ. With the even background and consistent contrast on the crisp edge and lack of shadows, editing this with the magnetic lasso tool took all of ten seconds.

Want to make editing the photographs much, much easier? If you can, find a large light box - many geology departments will have old large ones used for drafting cross sections and geologic maps, likely to be in mothballs thanks to the use of software like GIS. I'm a bit old fashioned and love to do lots of stuff by hand, and gleefully admit that I still use light boxes for drafting (my lovely wife - Hi Sarah! - got me a spectacular light box for my 30th birthday last fall). Back-lit fossils are super easy to edit in photoshop. What a light box achieves is a continuous light tone around your fossil, which makes editing the image and getting rid of the background (either through the magic wand tool or the magnetic lasso tool) 3-10 times faster. The flipside is that light boxes are expensive. Light boxes do another thing: they seriously increase the amount of light available for your camera - again drastically improving lighting conditions.

Basic tips 6: what to put your fossil on

This may be intuitive: anything you care enough to learn all this crap for is likely important enough that you don't want to damage it during the process of taking photos. If a fossil, use foam! Or sandbags. Since you're not storing the fossil permanently like this it is OK to use non-archival materials for a couple of hours. Fossils should be propped up so they don't fall over. Sand bags and wedges of foam are great for this.

The holotype skull of Tohoraata raekohao perched on a series of sandbags and foam blocks covered by a sheet of white tyvek, with a giant sheet of white styrofoam behind to provide a degree of backlighting for ease of editing, and of course diffused lighting from upper left.

Another consideration is what the background around the fossil will look like. Most are going to crop out the background in photoshop so that the pile of ugly sand bags and other random objects stuck together like a house of cards underneath your fossil aren't cluttering up your published image. How can we make this easier? For smaller specimens on a flat surface that won't stand the way you need , you can use a lump of plasticene clay (which can leave grease on your fossil) or playdough (which does not). It's best to not have any of this material visible to keep editing time down. Another trick is to use sheets of Tyvek, which is super thin and lightweight. For gods sake do not use black cloth! Black cloth doesn't reflect much light and produces much crappier lighting conditions often leading to underexposure of your fossil around the edges or in cracks along the periphery. If you need to build a large pile of styrofoam blocks and sand bags to jug up several bones or a large awkward one into an appropriate orientation, cover the whole thing with tyvek which can settle into all the nooks and crannies and voila! The monstrous 3D support pile you've meticulously constructed is now hidden and easily edited away!

A temporary diffuser made out of an ethafoam sheet and a piece of scotch tape...

Advanced tips 1: diffusers

Hard lighting can cast small shadows that may obscure some detail and increase "local" contrast in spots so that small highlights are overexposed and shadows are underexposed. Using a diffuser can scatter light and produce softer lighting. Diffusers can be purchased, but we're paleontologists - we're ingenuitive and often broke! Make your own diffuser and spend the money on a better lens instead. Diffusers can be made with sheets of vellum, mylar, or even tracing paper - anything thin and semi transparent works. Too much light coming through? Use another sheet! At Otago we had a number of different homemade diffusers made from a card matte from a picture frame with mylar or vellum taped in place, stuck onto a wooden base to keep it upright. Different sizes are great. For a large light that's on a tripod, you don't need to waste time making a four-foot tall diffuser: just get some sheets of mylar or vellum and use artist tape (the blue masking tape) and stick it directly onto your lamp! Also: make sure not to knock your diffusers over onto your fossil during photography if your fossil is precariously balanced. If you're shooting in a museum and don't have any of those types of paper, thin sheets of ethafoam can be used in a pinch.

...and a much better diffuser, seen at left, made out of vellum and a wooden frame. This is a better example since it also showcases the soft lighting produced.

Professional photographers who photograph small (e.g. jewelry) to large objects (e.g. people) often use light tents - which essentially is a 270 degree diffuser that also acts to provide backlighting. I'd love to try using one of these. Here's an example below, and here's a how-to guide on making your own light tent.

A collapsible light tent - from

Advanced tips 2: focus stacking

Can't get a fossil to be completely in focus? Short of increasing the amount of light you have and closing the aperture severely, sometimes some specimens just won't fully go into focus. Luckily there's a technological fix for that called focus stacking. If you take photos under the same lighting conditions with the focus set at different overlapping levels of the subject, you can digitally merge those using Photoshop or another program which takes the parts of your photos that are in focus and merging those whilst ignoring the parts that are out of focus. To take appropriate photos, you can 1) keep the focus fixed on the camera and slide the camera back/forth on a rail (expensive) or 2) just manually adjust the focus, taking 3-10 photos depending on how much of the subject is in/out of focus. Note: this will be more important if shooting with prime lenses at low F-numbers.

Focus stacking: image on left is one of five original photos. In this photo (holotype periotic of Tohoraata raekohao) the parts of the bone closest and furthest away are out of focus, while the middle of the bone is in focus; five photos spanning all parts of the subject were taken and then merged using focus stacking to produce a photograph with continuous focus (right).

Digital merging can be done in Photoshop CS5, CS6, and above, and tutorials for it can be found online - but very briefly, you load individual photos into photoshop as layers (adobe Bridge is the easiest way to do this) within a single PSD file, then go edit->align layers, and once that's done, edit->merge layers. Photomerge doesn't really work too well at this. There are other dedicated freeware programs, but from what I've tried they're all awful. All of my earbone photographs from my Ph.D. thesis on New Zealand eomysticetid whales were shot at different intervals and focus-stacked... literally over 100 different images composited from 4-12 separate photographs.

A large (but by no means the largest!) specimen being photographed in the stairwell at U. Otago; the block is the rostrum of a referred Tokarahia lophocephalus skull, and is positioned right next to the giant penguin Kairuku display case for those familiar with the Otago geology department.

Advanced tips 3: photographing large specimens

Large fossils - some dinosaurs and whales come to mind - pose a whole host of problems. Occasionally fossils are embedded into a wall of plaster or are in some sort of a mount - or worse, in a dark corner in a basement and are too large to move. In these cases, some creativity is needed with lighting and camera angles. For very large specimens, you can either use a very, very tall ladder (if available, say at an oversize facility like UCMP's Regatta building in Richmond, CA, or USNM's Garber facility in Maryland) and photograph the fossil on the ground. This means handheld shooting or the use of a swing arm that can clamp onto a railing. At U. Otago, we had no room for something like that, but we did have a very tall stairwell - so we'd literally place a whale on the floor at the bottom, clamp a camera onto the railing on the second story (first story had ~12 foot ceilings, so the camera was nearly 20' up). All of my photos of eomysticetid skulls for my Ph.D. thesis were taken like this.

If a fossil can be tilted so that you can shoot horizontally, even better! Just go far away from the fossil until everything is in frame and shoot horizontally as if it were a deer out in nature or something. If the specimen is too fragile, this option is probably not a great idea.

Can't fit a tripod or a flood light in because the fossil is too damned huge? Stick a white sheet or a large plank of styrofoam at the desired lighting angle, and aim a spotlight or LED lamp at the foam - and bounce the light off the foam at the desired angle (e.g. upper left). This is a workaround for photographing enormous specimens in cramped areas.

Sometimes you're stuck with a specimen that is too big to shoot from above and too heavy or large to move. The holotype skull of the eomysticetid Tokarahia kauaeroa is such a case - the basement ceiling at U. Otago is about 7' above the floor, and the block needs about six people to lift - it's quite scary to do so, and logistically a nightmare. So, we took photographs from the highest point possible using a tripod, and stitched the photo together. This ended up looking not quite as great as a photogrammetric 3D model I put together, so we ended up just using an arguably undistorted image derived from photogrammetry. Point is - creativity means that there is always more than one way to skin a cat (or dead whale).

An OKish photo of a cow shark upper anterior tooth, shot horizontally at UCMP (Berkeley) with my zoom/macro lens from about three feet away.

Advanced tips 4: photographing tiny specimens

Macro lenses and good lighting mean that you do not need to screw around with cameras attached to binocular microscopes. With a proper macro lens (a type of prime lens ideally suited towards closeup photos) you can take photographs of objects 4-15 mm in size with excellent resolution, no microscope needed. It's a great way to photograph the middle ear ossicles of whales and tiny shark and dolphin teeth.

I have a bit of a "ghetto" macro lens - it's a telephoto zoom lens with a macro lens feature. It can take great closeup images, but only from about 30-40 cm away at the closest. What this means is that it's really awkward to use this on a camera stand, and I have to get up on a chair to look through the viewfinder and risk falling over. So, rather than bother with all that crap, I set up my tripod, light, scale bar, and shoot horizontally on a table top. Problem solved!

Advanced tips 5: light temperature

When I was four I saw a light bulb turned on up close for the first time, and it was within reach, so I reached out my hand and touched it with my right index finger. It took a second before I realized the pain, and within minutes I had a pretty gross blister; I was a stupid child. Light temperature does not refer to how hot a bulb gets. Rather, different bulbs will produce a different color. Tungsten bulbs produce yellow light - and though most cartoons depict the sun as somewhat yellow, it is far from it - a blinding white light. LED lights look a bit blue in comparison to tungsten - but are actually daylight temperature. The point of all this is that if you care enough, it's perhaps best not to mix different temperatures - the two most common being daylight (LED, camera flash, halogen) and yellow light (tungsten bulbs). Note that this does not matter one bit if your final image is going to be converted to black and white. It *might* look weird if going for a color image, but most are not going to notice so this is something I never really worry about.

 Yours truly coating the holotype specimen of the sea lion Neophoca palatina for a paper with Morgan Churchill - coming soon in Journal of Paleontology. Note the glass place and cake turntable below; the glass plate allows blacklighting with a lightbox.

Advanced tips 6: ammonium chloride coating

Fossils that are dark brown or black pose a problem in that little surface detail will be apparent no matter what the lighting conditions are. An old school method to solve this problem is to coat a fossil with sublimated ammonium chloride. Ammonium chloride is mostly harmless and can be placed into a glass vessel that somewhat resembles a crack pipe: ideally it will have a small nozzle followed by an expanded bulb, and then a tube to which you can attach a little air puffer or a slow stream of compressed air. Solid ammonium chloride is placed into the bulb (which is unfortunate since the chemical looks like white powder) and then, even worse - you heat the bulb up over a bunsen burner or other comparable flame. It sublimes - in other words, goes directly from a solid to a gas - and a gentle puff of air pushes the gas out the nozzle, and onto your fossil - where it sublimates back into a solid, giving a very thin coating of white. This coating is easily removed with water - make sure your fossil can take a brief and gentle soaking to remove the ammonium chloride. Be careful though, it will come off on your fingers - meaning another spraying is in order. Some practice is necessary to get a nice even coating. Another tip: you do not have to start over fresh for each view. I would spray as much as possible on the first try, take the photo, flip the specimen, spray the other side, and repeat until everything is photographed. Remember the focus stacking described above? Each of my eomysticetid whale earbones was ammonium chloride coated AND focus stacked. Goddamn that was a lot of work. This is sort of unnecessary if you can publish in color, unless a fossil is really, really black like the inside of a black hole (phosphatized bones/teeth for example).

Bunsen burner and ammonium chloride in the glass tube, chemical is present in the bulb - you can see a bit of whitish gas escaping: this is what is blown onto the fossil.

Quick note: if shooting with backlighting on a light box, you do NOT want to pick up the fossil and so at Otago we would place the fossil onto a sheet of glass, coat it, and place the glass onto the light box so the light can still shine through.

At other institutions that will kindly remain unnamed, some sort of aerosol can spray crap has been used as a shitty alternative to ammonium chloride - but unless removed immediately, this stuff becomes rock solid and will not be easily removed except with diligent scraping. I've seen many fossils unnecessarily and potentially irreversibly harmed this way, and the hardened paint-like substance is nearly more difficult to remove than the actual rock the fossil was initially entombed within. Please, for the love of god, do not abuse your fossils like this!

Advanced tips 7: shooting in raw

DSLR cameras can shoot in two modes: they will save a jpg "preview" file - the image most digital cameras will produce - as well as a "raw" file. Raw files are difficult to edit and only a few programs can actually open them, and even those do not permit the image to be permanently tinkered with. Raw files are great because they can be adjusted and a jpg or tiff file generated from them, but no information is lost. In other words: if you want to increase contrast in a jpg and save the file, you lose information from that image and it is altered forever unless you have an original backed up someplace. With a raw file, the "sliders" in the program can just be reset and the image is never permanently altered. Essentially, raw files are "archival" image files. The flipside is that raw files are large, and may be a bit cumbersome to edit, and require specific image editing software. Different camera companies use different file types: Canon (what I use) uses CR2 files whereas Nikon uses NEF. Adobe Bridge can open up some (NEF). I personally hate software that isn't free, so I use the very flexible freeware program "RawTherapee". A word of caution: shooting in raw takes a lot of harddrive space; my Ph.D. dissertation folder on my computer has nearly 20 gigabytes of photos thanks to raw files.

Advanced tips 8: efficiency

Lastly, a word on efficiency. A good lighting setup can take anywhere from 10 to 45 minutes to set up, depending on how much room you have to set up, if you have help, or alternatively, have somebody in your damn way or distracting you. Or if all of a sudden it's afternoon tea and it would be rude to continue shooting. It takes a while to set up all of this crap, and it's not fun. Many, many arguments with my lovely wife were started by me taking too damn long to take all my thesis related photos on campus during my Ph.D. Hours spent taking photos without food or water plus bright lights is a great cocktail for a massive headache.

So: get an assembly line started and photograph everything you can over a few hours. This also really helps if you need to maintain consistent lighting; you may very well not remember how to mimic a certain lighting setup you had before (take a cellphone picture). This is especially relevant if you are taking ammonium chloride coated photos.

Don't get too caught up in the details; it's simply not possible to produce a perfect photograph, though many will try under the delusion that it is reachable. If you begin to think that you're wasting a lot of time doing some of this, perhaps you're right! Think about how you could work around a particular problem or how to be more efficient. Photography is not art - I'm sorry to photographers, but after doing a fair amount of it, it takes a tiny fraction of the amount of skill required for fine art. What I mean is this: there's nothing really special about it, and a fair amount of judging of photograph quality is a bit of a black art and fades quickly into the realm of minute subjectivity. Photography is easy to learn, and anybody can read what I've written and use these tips to produce better quality images. Photography is mostly scientific, but bending the rules to get a better picture - or the same quality picture for less effort - requires a bit of creativity.

Further reading:

The Fossil Forum: Fossil Photography subforum

Photographing fossils PDF by Wayne Itano

Photographing Burgess Shale Fossils by Royal Ontario Museum

High Dynamic Range photography in Paleontology by Jessica Theodor and Robin Furr in Palaeo Electronica