A Pigment of our Imagination?

Trace metals as biomarkers for eumelanin pigment in the fossil record.
Today we publish our most recent research in Science Express (the online arm of the journal Science). Our team has been able to show a remarkable relationship between copper and pigment within exceptionally preserved fossils of feathers and other soft tissues.

Fig. 1. False color chemical image (left) of an approximately 120 million year old fossil of Confuciusornis sanctus, the oldest documented avian species to display a derived beak, with superimposed model of a eumelanin-copper chelate complex. The image was produced using synchrotron rapid scanning X-ray fluorescence. In this image red corresponds to copper and the distribution of this metal shows the patterns of original eumelanin pigments in this extinct species, thus allowing a reconstruction of pigment shading. Blue corresponds to calcium in the fossil bone, and green is zinc within the sedimentary matrix. 

The results include important species such as the oldest beaked bird yet found, the 120 million year old Confuciusornis sanctus, and also the 110 million year old Gansus yumenensis, which looks similar to the modern Grebe and represents the oldest example of modern birds.

Pigment is a critical component of colour. Our team can map the presence of pigments over whole fossils, revealing original colour patterns (but through a monochrome filter). Our findings indicate that pigment chemistry holds the future key to the ultimate goal of discovering the full colour palette of past life, from dodos to dinosaurs and beyond.

Colour has played a key role in the processes of evolution by natural selection that have steered all life on Earth for hundreds of millions of years. Whether this be sexual selection or camouflage, colour and patterning plays an important role in the struggle to pass one's genes to the next generation....else many top clothing brands would be bankrupt, given our own species desire to look gorgeous!



Fig. 2. Synchrotron rapid scanning x-ray fluorescence image of the calcium distribution in a fossil specimen of Confuciusornis sanctus, an ~120 million year old avian species, the oldest documented to display a fully derived beak. Calcium is high in the bones as shown by the bright white areas, but calcium is also high in the areas corresponding to residue of downy feathers in the neck region. This is interpreted to be due to the distribution of calcium being controlled by eumelanin chelates in the neck feathers, indicating that these soft tissues were originally darkly pigmented.


This unique scientific breakthrough can allow paleontologists and biologists to reconstruct pigment patterns in extinct and living animals respectively, as well as provide an understanding of the way in which biological compounds are preserved in specific environments through geological time.

This could provide a far greater understanding of the feeding habits and environments occupied by extinct creatures, as well as shedding light on the evolution of colour pigments in modern species. Here the data from living species was so crucial to deciphering the chemical code locked in deep time.

Roy Wogelius

Fig. 3 (Left) Collage of images. Top, optical images of: blue jay feather, squid, and fossil fish with feather. Bottom: x-ray images showing the distribution of copper (red) in the same organisms. Copper in the dark parts of the feathers, the fish eye, and the squid ink sack indicates the presence of eumelanin pigmentation and in combination with other elements can be used to map pigment distributions in fossils and existing organisms. 


The X-ray team, led by Dr Roy Wogelius, Dr Uwe Bergmann and yours truly (‘Dr Phil’), took the unique approach of using the super-bright x-ray light of a synchrotron to analyse the soft tissue regions of fossil organisms. The application of X-ray physics to palaeontology has shed new light on this tangled tale of prehistoric pigments in deep time and how to map and recognise specific chemistry in fossils that are hundreds of millions years old. Roy Wogelius, lead author on the paper and University of Manchester geochemist, said: “Every once in a while we are lucky enough to discover something new, something that nobody has ever seen before. For me, learning that copper can be mapped to reveal astonishing details about colour in animals that are over 100 million years old is simply amazing. But even more amazing is to realize that such biological pigments, which we still manufacture within our own bodies, can now be studied throughout the fossil record, probably back much further than the 120 million years we show in this publication.”

To unlock the stunning colour patterns, the Manchester researchers teamed up with scientists at SLAC National Accelerator Laboratory (USA) and used the Stanford Synchrotron Radiation Lightsource to bathe fossils in intense synchrotron X-rays. Also working on the synchrotron team were Pete Larson, Holly Barden, Nick Edwards, Bill Sellers and not forgetting SLAC's Sam Webb. As I have mentioned before, this type of experiment runs 24 hours a day for a week…so is the ultimate sleep deprivation study. Without a large support team of colleagues, we could not undertake such exciting research. Several other team members made major contributions to the acquisition of material and its analysis back in Manchester.

Phil Manning (left) and Uwe Bergmann (right)

The key to their work was identifying and imaging trace metals incorporated by ancient and living organisms into their soft tissues, in the same way that all living species do today, including humans. Eumelanin pigment has a copper atom at its structural heart, allowing us to map its presence, via its distinctive signal. Eumelanin is possibly the most important pigment in living species and our study clearly identified this pigments presence and distribution in several extinct species. We can now use this copper-coordinated molecule to help unlock the pigment palette of man other extinct species.

Without essential trace metals, key biological processes in life would fail and animals either become sick or die. It is these essential trace metals that the team has pinned down for the first time.



Fig. 4. (above) Shown here is an artist’s conception of the pigmentation patterns in Confuciusornis sanctus, an ~120 million year old species, the oldest documented to display a fully derived avian beak. Patterns are based on chemical maps of copper and other trace metals in several fossils of this organism. Trace metals, copper especially, are found to exhibit patterns which reveal eumelanin pigment distribution in the living organism. In the background is a picture of one of the fossils used to derive the artist’s drawing. Drawing of C. sanctus is by Richard Hartley, University of Manchester.


It is fair to say that the fossils we excavate have even more potential to unlock secrets on an organism’s life, death and subsequent events impacting its preservation before and after burial. To unpick this complicated chemical archive that fossils represent, can only be achieved through the hard work of multidisciplinary teams that can bring in to focus many areas of science. In doing this, we can unlock much more than just palaeontological information; we now have a chemical roadmap to track similar pigments in all life.

Our results clearly show that chemical remnants of pigments may survive even after the melanosome (biological paint pots) containing pigment has been destroyed. Some of the samples they publish clearly preserve a chemical fossil, where almost all structure has been lost in the sands of time. The chemical residue can be mapped to reveal details of the distribution of dark pigment (eumelanin), probably the most important pigment in the animal kingdom.

Bill Sellers (left), Holly Barden (centre) and Uwe Bergman (right) check alignment of specimen on stage.

This pigment gives dark shading to human hair, reptile skin, and bird feathers. Using rapid scan X-ray fluorescence imaging, a technique recently developed at SLAC, our team was able to map the residue of dark pigment over the entire surface of a large fossil, for the first time giving clear information about fundamental colour patterning in extinct animals. It turns out that the presence of copper and other metals derived from the original pigment gives a non-biodegradeable record of colour that can last over deep geological time.

Nick Edwards (left), Roy Wogelius (centre) and Holly
Barden (right) glove-up for action!

Uwe Bergmann, SLAC physicist and co-author on the paper said: “Synchrotron radiation has been successfully applied for many years to many problems. It is very exciting to see that it is now starting to have an impact in palaeontology, in a way that may have important implications in many other disciplines. To work in a team of such diverse experts is a privilege and incredibly stimulating. This is what science is all about.”

Using this novel method to accurately and non-destructively measure the accumulation of trace metals in soft tissues and bone, the team also studied the chemistry of living species, including birds. Roy Wogelius added: “This advance in chemical mapping will help us to understand modern animals as well as fossils. We may also be able to use this research to improve our ability to sequester toxic materials such as radioactive waste and to devise new strategies for stabilizing man-made organic compounds”.

The synchrotron at SSRL has been used for many years to probe the innermost workings of molecules to an almost impossibly small scale. The team from the University of Manchester and SSRL has shown it is possible to retain the sensitivity and probing ability of the synchrotron, whilst working at a much larger scale (these fossils are giants in terms of synchrotron samples). The information gleaned from the current study is way beyond anything we could have dreamed of a few years ago.

Pete Larson (left) and Uwe Bergmann (right) prepare
another fossil run in the beam line station.

The potential for this technique to gently un-pick the chemistry of long extinct species is quite breathtaking. The possibility of mapping biosynthetic pathways, enzymatic reactions and mass-transfer of elements between organic and inorganic systems through deep time...offers many areas of science, not just palaeontology, cracking insight to the past. More importantly, the hindsight that the fossil record provides will undoubtedly have benefits for understanding Earth processes, both today and in the future. Advances in one field are often the function of a curve ball from another.


Take a look at our podcast on the Science web site, just click HERE to link to Roy and I talking about this research.


A final reminder that 'In Living Colour' will be transmitted on the National Geographic Channel in the USA at 10pm EST on Thursday July 7th. You can watch Uwe, Roy and I...along with many other folks in our team, take a close look at colour in the fossil record.

Once more into the field......

It's June. The mosquito larvae have transformed into the adult bloodsucking fiends....so it must be nearly time to go back into the field. The mosquitoes must be hungry for the blood of an Englishmen.....again. Last year I must have single-handedly boosted the Culicid population for the whole of South Dakota....I am sure this year will be no different. Whilst my colleagues work unaffected by the beasties that bite and suck, I am like a walking target and blood donor rolled into one.

Bleak but beautiful, the Badlands of the Hell Creek Formation

We will have a smaller team in the field this year, around 6-9 folks. We hope to survey and record our new site that we discovered last field season. This will entail laser-scanning the whole outcrop....using a fancy new laser surveying device, called a LiDAR, short for Light Detection And Range. This one is being loaned to me, so we have to look after it... especially as replacing it might cost $80,000....yikes.

Using a LiDAR laser scanning unit in Fumanya (Spain) to track dinosaurs.

We have already used LiDAR before to map track sites and even to 'weigh' dinosaurs, or at least measure their volume from mounted skeletons and then calculate their body mass with a simple bit of arithmetic. This technology has multiple uses in the field this year, but its primary function is to provide a 3-dimensional digital outcrop model that we can plan all the major excavation, environmental impact and site remediation with for next year. We can also place all the data we collect this year, into a fancy 3D model, providing us with a chunk of virtual Hell Creek Formation to visit from the comfort of our office's in UPenn and Manchester....where there are NO mosquitoes.

Dinosaur!......What Dinosaur?

As with last year, I will endeavor to keep a daily fieldwork diary for one and all to experience the heat, bugs, exhaustion and sheer delight of plucking beasties from the Earth.

'Life in Color' or 'Life in Colour'?

National Geographic have kindly brought one of the shows from the 'Jurassic CSI' series forward in transmission to July 7th on the NG main channel. It will be the first of the six shows to be aired in the USA, the rest following from mid-August through September 2011. It's strange seeing something on the box that was filmed nearly two years ago, in some cases. However, it will hopefully provide an injection to the growing number of documentaries about palaeontology that show 21st Century technology being applied to this broadening field of science.

The 'In Living Color' (spelt minus the 'u' for the US market) will explore some of the latest research that has been undertaken between the University of Manchester and the Stanford Synchrotron Radiation Light-source (SSRL). You will see Roy Wogelius, Bill Sellers, Uwe Bergmann and myself applying our disparate (that's not desperate!) skills to precious fossils from around the world. Worth a watch if your in the USA.

I feel remiss that I did not mention a couple of weeks ago, I finally managed to see the horseshoe crab (Limulus polyphemus) making 'whoopy' on the Delaware shore...in their usual vast numbers! A remarkable mass mate/spawning that occurs every year on this long section of the Atlantic Coast of the USA. On both full and new moons through May and June, this incredible spectacle can be seen almost anywhere along the Delaware and New Jersey shore. These wonderful beasties drag themselves up onto the beaches in their millions, dumping BILLIONS of eggs, to ensure the next generation. I will endeavor to sort my images from this wonder of nature and tell you more about this enigmatic creature, whose ancestry long pre-dates dinosaurs.

Blogging with Dinosaurs

Time disappears a little too quickly when your very busy, but still having fun! Fifty Seven blogs later and a year has passed and I am stilling finding time to write about the wee timorous beasties (such as Archaeopteryx below)...not all were so 'wee' I suppose.

The bulk of my time these past few months spent organising this year's field season and writing-up research. I will soon have teams of palaeontologists, biologists and geologists coming from the UK, Spain and the USA to help dig a site that we have in the Hell Creek Formation. This will keep my field team and I up to our armpits in dirt, a happy place, while the Jurassic CSI series is transmitted in the USA.

Planning for the excavation has several hoops that needed to be jumped through...all very necessary. Earlier this year I had to complete formalities with the suitable authorities to arrange access to the said dig site. This has been done and we are now waiting for the final say on the excavation paperwork.

Funding such excavations is not much fun. The economy is hardly booming and this impacts directly on many areas of research, especially in the UK. Last year I had to use my own savings to keep some of my field team in South Dakota. I should say, it is not uncommon for palaeontologists to dip into their own pockets to fund digs. I am still hunting for funds from various places to see if I can keep the 18 folks on my field team in a mosquito populated, arid, windy, sunburnt, dirt-shifting 'heaven' for a month.

For those of you who have been following the blog from last May, a big Thank You! In the past year you will have read how palaeontology can comfortably hold its head high, when it comes to the relevance of our research to everyday life. The information that we are now able to glean from the fossil record is influencing many fields, including; climate research, the burial of waste, long-term storage of radioactive waste and the impact of oil spills and suchlike on living species and many other crucial areas.

Whilst our research is firmly anchored in the past, we set our sights on its application to the future.

Seeley, dinosaurs and divisions...

Harry Govier Seeley gave us something that neither Huxley, Cope nor the infamous Marsh could (but this was not from a want of trying). In 1887 H.G. Seeley gave us the lasting major division within Richard Owen's tribe of beasties, giving us the saurischian and ornithischian dinosaurs. You have already met the tooth and claw of the saurischia ('lizard-hipped') that ultimately gave rise to all birds today. Now this is the rub, the ornithischian ('bird-hipped') dinosaurs have nothing to do with birds, other than being the sister group to the saurischia that did...confused? When folks say, 'Whats in a name', maybe here hindsight would have made Seeley chuckle. His division is robust, but the names often confusing, given each groups evolutionary products...sadly zero for the ornithischian dinosaurs post-Cretaceous. One thing about this group, if you visit the AMNH in New York, you'll get to see some of the most important ornithischian fossils from north America. Here is a brief tour of the said gallery.

Triceratops with its distinct horned face and solid frill has been having a rough ride with its contemporary Torosaurus... identifiable from its larger perforated frill. Jack Horner and colleagues have recently suggested the latter is an adult of the former...'slaying' a species with a stroke...or should I say 'stage' of ontogeny (growth).  This is not a new approach to slaying dinosaur species, as Peter Dodson did the same back in 1975 with his analysis of hadrosaur skulls...reducing nine to three species in a stroke. However, folks must have been more careful when naming species since Peter's work back in 1975...or have they? Other palaeontologists have urged caution, such as Mike Benton at Bristol, who also suggests that ~50% of dinosaur species might not be valid! Something to think about when we explore museums, their collections and the barren Badlands when hunting 'new' species...or maybe just another growth stage. Lets just say, we must be careful when naming new species of dinosaurs.

However, my favourite fossil in this gallery is not something horny from the Cretaceous, but wrinkled hadrosaur (Edmontosaurus) that looks like it overstayed its welcome at a sun-bathing contest. This 'beautiful' fossil was dug-up by the royal-family of palaeontology collectors, the Sternberg's...as this was a family of fossil hunters extraordinaire!

When you stand above this remarkable dinosaur, with its arms and legs wide open and its chest caved in...it looks almost too incredible to be 65 million years old, but that is exactly what it is, incredible and 65 million years old! What is most amazing for me, Charles Sternberg and his two sons prepared the fossil, as you see it today, while still in the Badlands of Wyoming.

When dinosaurs are not fully grown, they really can fool us...this skeleton has been given several names in the past, but now most agree it is either a juvenile Lambeosaurus or Corythosaurus! This is possibly why our research group has concentrated on understanding more about the preservation, biomechanics and anatomy of these enigmatic beasties. I shall add some more on my visit to the AMNH ornithischian gallery soon!

Long overdue AMNH visit!

Oh how time disappears quicker than a rat down a drain-pipe...It seems only last week that I was promising images of the American Museum of Natural History )New York), but failed miserably at getting back to my blog...until now!

Just entering the museum provides you with a stunning dino-tastic diorama...and that's before you even have to part with any money! If you get a chance...just stand underneath this vast animal and look straight up. Some dinosaurs were not just big, they were huge...

The dinosaur galleries are something to behold and have long been a favorite of mine. This is where I shall pictorially take you now.

The dinosaurs are divided into two main halls, one saurischian and the other ornithischian...lets start with our friends the lizard hipped beasties.

Here Apatosaurus ambles along in some Paluxy River (Texas) sauropod tracks....quite apt! Opposite is a theropod...

...possibly my favorite large predator from the Jurassic...which always leaves room for the skull and skeletal mount of possibly the most famous, or should I say infamous, predatory dinosaur in the world.....

...yup, Tyrannosaurus rex. This is the skull that we all want to see....well, almost! I have to admit there are other stunning predatory dinosaur fossils in this exhibition, some who lack in size, make-up on tooth count to cause major trauma...such as my favorite small theropod, Deinonychus.

However, before I depart on a Cretaceous note, why not end on a rather important predator from the Triassic of Ghost Ranch (New Mexico). A great location name, filled with beautiful fossils of one of the earliest predatory dinosaurs, Coelophysis...

Last and certainly not least...we must not forget the strange theropods from Mongolia, no...not Velocirapter, as they are not that strange at all, but jumping beak-first into the theropod (I forgot my teeth) strangeness awards, is Oviraptor...

...perched, or should I say 'nesting' on a clutch of eggs. This mis-named dinosaur, mistaken for an egg-thief, should have been named 'Ovimaiasaura'...the 'egg-good-mother' dinosaur!

It would be unfair to show you all the saurischian dinosaurs at the AMNH, as you HAVE to visit there if you ever find yourself in New York City. Now...that is enough tooth (toothless) and claw for one day. Tomorrow (I hope) I will take you to the land of bird-hipped dinosaurs, the ornithischians at the AMNH.

Caught between continents!

My blogging has fallen by the wayside these past few weeks. The day after my visit to the AMNH I had to dart over to the UK to put a Gobi dinosaur vertebra on the X-Ray CT spit, then jump on a plane to Germany to give a paper at a wonderful meeting in Obernkirchen. I then had to hop back on a plane to the UK, via Zurich...spending a night writing-up a paper with a colleague in Manchester, before heading back to the USA the next day...and that's when I started getting busy!

Close Encounters of a Saurian Kind....A night a the Obernkirchen Dinosaur Track Site in Lowe Saxony.

I realize that I have a great deal of blogging to catch-up with...I shall endeavor to do this at the weekend....now let me think, what day is it today?

A day at the Museum.....

I find myself sat in a coffee shop, en-route to New York City...realizing that I have not written my blog for a couple of weeks! The wonder of free WiFi comes to my rescue. To be honest, I have been buried with work these past few days...yes, the usual. Reviewing and writing papers, teaching and also completing my BLM permit application for this summers excavation in the Hell Creek Formation (South Dakota). As always, life is never dull, just busy.

So, why New York? That's easy to answer, as located there is one of the museological gems of the world, The American Museum of Natural History (AMNH). I shall not be alone on this pilgrimage, as I have a group of undergraduate and graduate students from the University of Pennsylvania along with me. They too share my enthusiasm for this historic institution and its incredible collections. No less than the first Tyrannosaurus rex arrived here in the first gasp of the 20th Century. The then assistant curator, Barnum Brown, excavated this 'Coca Cola' of dinosaur brands into the world, but his boss Henry Fairfield Osborne was responsible for naming it in 1905. Thankfully, the name has stood the test of time, unlike the unfortunate case of Brontosaurus...a long 'tail' I must recount at some point.

The AMNH became even more famous, if that were possible, after the release of the film, 'A Night at the Museum'...a splendid tale of bones that go bump in the night. The said film was set in the hallowed halls of the AMNH, with its impressive outlook on Central Park. However, when visitors first make their way up those famous museum steps and in through the grand front entrance off Central Park...they are met with a very different museum from that seen in the Film. This is simply because all the interior shots for the said film were shot elsewhere on an artificial set....you cannot blame the AMNH for this. Imagine the chaos of filming a Hollywood movie inside one of the most popular visitor attractions in New York. Impossible!

Tomorrow, I shall endeavor to take you on a pictorial tour of my 'Day at the Museum'.

50 Million year old Reptile skin....splendid!

Today the University of Manchester Palaeontology Research Group  published another paper in the journal Royal Society Proceedings B. The subject of this paper, some beautifully preserved reptile skin. The brightly-coloured image below shows the presence of amide groups – these are organic compounds (building blocks of life) – in the ancient skin of a fossil reptile, found in the 50 million year-old rocks of the Green River Formation in Utah, USA.

This image had never been seen by the human eye, until our team, in this case led by Dr Roy Wogelius and graduate student Nick Edwards, used state-of-the-art infra-red technology to reveal and map the fossilized soft tissue from this beautifully-preserved reptile.

These infra-red maps are backed up by the first ever element-specific maps of organic material in fossil skin generated using X-rays at the Stanford synchrotron in the USA, working in collaboration with Dr Uwe Bergmann at SLAC. This is the same technology that was used to hed light on the chemical ghost of feathers preserved in Archaeopteryx, published again by our team last year in PNAS.

Chemical details are clear enough that we able to propose how this exceptional preservation occurs. When the original compounds in the skin begin to break down they form chemical bonds with trace metals, and under exceptional conditions these trace metals act like a ‘bridge’ to minerals in the sediments. This protects the skin material from being washed away or decomposing further...literally a fossiliferous hard-hat!

Roy is as chuffed as ever about the results, saying, “The mapped distributions of organic compounds and trace metals in 50 million year old skin look so much like maps we’ve made of modern lizard skin as a check on our work, it is sometimes hard to tell which is the fossil and which is fresh.”

Roy is also keen to point out to the palaeontological community that, “These new infra-red and X-ray methods reveal intricate chemical patterns that have been overlooked by traditional methods for decades.”

The new images are compelling, and represent the next step in our research programme to use modern analytical chemistry and 21st century techniques to understand how such remarkable preservation occurs, and work towards discovering more on the fossil chemistry preserved in ancient life.

These new results imply that trace metal inventories and patterns in ancient reptile skin, even after fossilisation, can indeed be compared to modern reptiles. The infra-red light causes sweet vibrations in the fossilized skin, and a map of where these vibrations occur can be obtained from a fossil by using a trick: a tiny crystal (like an old phonograph record stylus) which moves from point-to-point in a programmable grid across the surface.

At each point where the tiny crystal touches the fossil, an infra-red beam that shines through the crystal reflects off of the crystal base, but a small amount of the beam probes beyond the interface- and if organic compounds are present, they absorb portions of the beam and change the reflected signal.

This has allowed our team to non-destructively map large fossils which do not themselves transmit or reflect the beam – a revolutionary process for paleontologists.

Nick Edwards, first author on the publication, said: “The ability to chemically analyse rare and precious fossils such as these without the need to remove material and destroy them is an important and long overdue addition to field of palaeontology.

Here physics, palaeontology and chemistry have collided to yield incredible insight to the building blocks of fossilized soft tissue. The results of this study have wider implications, such as understanding what happens to buried wastes over long periods of time. The fossil record provides us with a long-running experiment, from which we can learn in order to help resolve current problems.


You can learn more about this discover on a video podcast with myself and Roy! Just click HERE

...that's funny?

Last week was fun. In a fossil-kind of way...where I had time to sit down and talk with colleagues from across the many departments and faculties at Manchester who make-up the Palaeontology Research Group. From Mike Buckley with his protenacious approach to palaeo, Bill Sellers bounding forward with his locomotion work, Bart van Dongen blasting organic molecules into revealing their identities with his thermal hammer (Pyrolysis unit!) and Roy Wogelius burying his head into surficial processes at the atomic level on squished animals now entombed in rock....precious fossils. I also managed a quick dash to Paul Mummery's x-ray CT emporium, but alas he was off to Oxford with my palaeo-computational colleague Lee Margetts. All these folks and more make-up the unique, some say quirky, group that is the University of Manchester Palaeontology Research Group.


As I have said in prior postings, it is this cross-faculty, multidisciplinary nature of our group that has been the secret to our success. We have all found common ground in long dead beasties...or 'fossils', as some prefer. The most important aspect of this group for me, is what I have learnt from these diverse disciplines, changing the way I conduct, collaborate and manage my research. The fact that I am now happy to talk about the interaction of intense monochromatic synchrotron x-rays with the electronic orbitals of atoms and the associated x-ray induced K-L shell transitions of electrons in fossils,...has simply reinforced how important collaboration is with scientists from outside my discipline. I feel privileged that my knowledge has significantly broadened, but at the same time my understanding has deepened. This is a function of both patient and good colleagues. 


Isaac Asimov, a brilliant (possibly the greatest) science fiction writer and an excellent scientist to-boot, once said, 'The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...'


It great working with a group of scientists that at almost every twist and turn in our research we meet curious results that engender a similar Asimovian response. However, the key in our group is having the broad expertise to follow-up with sensible hypotheses that can then be tested and validated, before we go public on those 'funny' moments.

Dear Diary......

On Sunday night I head to Manchester. Once again I face the gauntlet of airline seats so vast that a garden gnome would feel claustrophobic, this combined with an atmosphere so thick that a very sharp knife would be required to even dent the said fuselage smog. The mere thought of airline food has me reaching for my supply of melatonin in the vain hope I will sleep through the optimistic nudge from flight staff asking that I partake in there wares. At times like this, I recall a French PhD student's comment while on fieldwork in the UK. I asked him his view of British Cuisine, his thoughtful reply was, 'Phillipe, this is not cuisine; this is food'...this makes my airline food by comparison look protenacious at best. If....a large 'IF' underlined in bold ink, with large flashing lights...I manage to nod off to sleep, I always end-up precisely folded into my available space like a piece of well-packed, pre-assembly Ikea furniture. The uncomfortable 1 or 2 hours of sleep (at best) is always broken by the announcement of our impending arrival to UK shores...an unhelpful one hour in advance of landing...I beg airlines to let us economy class folks sleep till 10 minutes before we start our descent, in the same way that they allow business class passengers! I was not aware that the upgrade correlated with how much sleep you were allowed on a long-haul flight. I often look enviously at the light blue drapes that lead through to the peaceful world of business class, where the dim-lit cabin affords its occupants those precious extra minutes of slumber.

As soon as we hit the tarmac at Manchester Airport, it's off to the University of Manchester to work through my haze of jet-lag. I'm sure that the US military sleep-depravation exercises did not feel this bad. My schedule next week is complex...I say 'schedule' now, given each time I asked a US colleague to share their diary with me, this was met with a frightened expression, often with rapid recognition that another 'British-ism' had crossed their path. A diary is a very private 'dear diary' kind of place in the USA...and is nothing to do with a schedule... pronounced 'sked-duel'. I tried arguing that this was pronounced incorrectly and should always be a 'shed-duel'....this is usually met with disdain and the follow-up of 'So, which 'shool' did you attend to learn English?'. My reply to that is, 'In an English 'shool' in Wells, England...where they taught me to speak English'. Churchill was right, we are 'two countries divided by a common language'.

However, back to my diary! The week will be driven by working through a PhD thesis recently sent to me to proof-read by one of the graduate students I co-supervise at Manchester. This will be punctuated with many meetings, the CT scan of a Gobi dinosaur's twisted vertebra, pyrolysis gas-chromatography mass spectrometry of some dinosaur fossils and a podcast. The latter is with a team from the Royal Society (London)...a function of a research paper that will soon be published in one of their journals. More on the contents of the said paper later, now...I must pack.

Dr Scott, Dr Phil and the Orange T. rex

Today I had the pleasure of giving a public lecture at the Philadelphia Academy of Natural Sciences. Little could have prepared me for the teeming hordes of 4-7 year olds clambering past and over each other to gain a glimpse, or maybe even a touch of the sacred hide of a rather fluffed-up orange T. rex...no, this was not a mad dream, but the telle-tubby-like reality that was 'The Dinosaur Train'.

I snuck into the back of the lecture theatre where I would give my talk in an hour. I was met by a packed auditorium listening to Dr Scott Sampson talking dinosaurs. Dr Scott is a real 'Dr' of palaeontology..a well-respected and extensively published scientist...who took the leap, like myself, into the world of the media. I choose documentaries with National Geographic, the History Channel and the good old BBC, Dr Scott choose pre-school TV...brave Dr Scott. However, we both choose public engagement in science as a major part of our careers. His scientific work truly rocks, but I think even he was surprised at the size of his audience...most were under 3 feet in height. With a maximum average height of 3'6''...the tales of nesting raptors and the important message that birds were dinosaurs was being swamped by the mutual diminutive wish that a 5'4'' orange T. rex going by the name of 'Buddy'...would soon join the erstwhile host of the said show...our friend Dr Scott.

I stood mesmerized at the back of the auditorium. Dr Scott valiantly pushed-on with his talk as the excited chatter of 'where's Buddy', gradually increased in volume among the expectant crowd. From a cracked door in the corner of the auditorium I'm sure I spotted a nervous human-head poking out of the top of a bloated orange dinosaur body...that was about to be fitted with a bizarrely enlarged theropod dinosaur head, complete with bulging eyes...I was not sure if this was a function of the fear levels being felt by the incumbent of the said costume. Having worn such a dino-outfit myself back in my Yorkshire Museum days, I was well aware of the kicking, pushing, thumping, dino-tipping antics of children...and their parents. I would just like to point out to all parents out there, that when a dino-suit wearing person is kicked over and is lain helpless on their backs, it does not look cute and is definitely NOT a photo-opportunity.

As Dr Scott summed-up his lecture to the listening parents, he hailed the coming of his good friend, Buddy. Huge gasps and screams were let-out by the waiting throng as the giant soft-toy gingerly entered the theatre...was that a timid step back towards the entrance? My heart went-out to the orange velour-clad student who had clearly been assured that this 'event' would look great on their CV...but maybe without the picture. You can imagine the line in the said CV, 'I took part in a major palaeontology open day at the Philadelphia Academy of Sciences, where I actively engaged with children from many areas of the City'... beats saying, 'I dressed-up as an orange T. rex and was chased around the building by thousands of screaming, over-excited kids'.

As the teaming hoard ebbed slowly from the room, I'm sure I heard Buddy scream for help...as the said dumpy-dinosaur was chased to the upper floors of the building by never-ending tide of kids. Every now and then a staff walkie-talkie would report on Buddy's current location...the hunt for the orange T. rex was merciless!

I looked down at computer screens and at the content of my lecture. Then I looked-up at the audience. I looked back down again at my lecture and realised that the 'Dinosaur Train' had cut my usual expert audience of 9 year olds to a mixture of toddlers, confused parents and exhausted Academy staff. My title of 'Blasting dinosaurs into another dimension'...and more importantly the content of my lecture... suddenly looked impossibly difficult. My slide of an atom, with its simple nucleus and careless orbiting electrons, now looked like quantum mechanics... and my birds-eye view of a synchrotron...might as well have been the blue-print for space ship design a long way away in the dim and distant future. I hastily re-wrote my talk in my head and looked at how much stage space there was for Monty-Python style silly walks...this would be a short 45 minute talk...more like 30 minutes!

I was introduced to the expectant audience. The lecture theatre lights dimmed, I took a deep breath...and stepped into the jaws of a battle-ship grey T. rex...bring back Buddy...I might just need him!

Chicken Curry, dinosaurs & Chemistry?

It was a standard busy day at the University of Manchester, combined with a swift lunch-time shuttle to the Royal Northern College of Music. Finding decent places to eat at the University is a constant quest for many academics at Manchester, thankfully there are many places from the Buisnes School to Geography were the trail for cuisine often ends in food. However, this particular day had chicken curry on the menu in the Music School, so the usual gathering of geologists from the School of Earth, Atmospheric & Environmental Sciences (SEAES) were loading their lunch trays with the said British favourite...fish and chips has long been knocked-off as the top favourite for some time by curry. At that time I was quite new to the said department, having just been appointed between the Manchester Museum (University of Manchester) and the SEAES. I sat at a table with one of our planetary scientists (Prof. Jamie Gilmour), an environmental geochemist (Prof. Dave Polya) and an inorganic geochemist (Prof. Roy Wogelius)...it was the latter who has since provided me a paradigm shift in my understandings of the preservation of dinosaurian beasties from days gone by.

Dr Roy Wogelius (foreground), Dr Peter Morris (left to Roy)
and Tyler Lyson (right)

As we sat inhaling our food, as time was short for lunch, I threw into conversation that I had just started working on a 'mummified' dinosaur. To have both the words 'mummy' and 'dinosaur' in a single sentence made all three look up and, albeit for a brief second, appear almost interested in palaeontology. I was getting used to the dry wit and humour of the three, so I waited for the barrage of quips on fossils not being what they used to be, or that the Late Cretaceous embalmers chasing dinosaurs and sticking natorn (Egyptian embalming salts!) where the sun would no longer shine! Dave Polya did not let me down on this front as he sat pondering the mechanics of inserting large quantities of salts up dinosaur rear-ends...However, Roy was sat opposite me and stopped eating, 'Do you want to know find out how the skin of your dinosaur got persevered?', Roy's question was one I had much pondered since seeing the bizarre preservation of Tyler Lyson's amazing find. 'I can help you Phil, if you can get me some samples'...this was the start of my journey into inorganic and organic geochemistry.

Fossil 'skin' from the 65 million year old dinosaur from
the Hell Creek Formation (North Dakota, USA)

I realised quite quickly that Roy had a healthy disrespect for palaeontology (or more precisely many palaeontologists)... something to do with an early college experience and a dance involving ping pong bats and an extinct group of arthropods called eurypterids. Having worked on eurypterids for my masters degree...I quickly change the subject when this experience is raised in conversation. This had clearly harmed Roy in some deep way. However, lucky for me Roy had spent the ensuing years becoming a leading geochemist. His realm of x-ray defraction, synchrotrons and infrared spectroscopy, was about to open-up the invisible sides of the electro-magnetic spectrum for me...a realm that would soon include the analysis of one dinosaurs particularly tough hide from late Cretaceous North Dakota. Since the 'Chicken Curry' moment in 2006, Roy has helped open Pandora's taphonomic box...taphonomy literally meaning 'burial-laws'..a science that we are beginning to play a small part in translating fossils into the processes that lay behind their preservation.

Sunlight and Synchrotrons

The snow has started to melt. The temperature is beginning to rise above freezing in Philadelphia for the first time in weeks. Leaves are starting to shoot and the grass is turning from rust-brown back to green. The organic geochemistry of life is re-booting for Spring. Sunlight is doing its job on these new shoots, fuelling the photosynthetic pathways that convert carbon dioxide into carbs...sunlight is a powerful source for the essence of life, energy.

Palaeontology has also started using light, in ways that I would never have guessed early in my career. We too are relying upon an interaction with light, but not with sunlight and plant chlorophyl, but with the surface of beautifully preserved fossils and more invisible parts of the electromagnetic spectrum.

Todays blog I thought I might bring-up the subject of a more familier part of the electromagnetic spectrum to many of us, X-rays. For many, their first interaction with X-rays is not a pleasant memory...as hospitals tend to come to mind, along with broken limbs! However, since September 2007 I have been getting used to another, more intense source of X-rays...those generated by synchrotron radiation. The synchrotron at which my group and I work is based at Stanford University (California) and is called the SLAC National Accelerator Laboratory.

SLAC from the air

You may recall in an earlier blog I was working crazy hours (20+ days) along with the rest of the Manchester team, basting fossils with X-rays...this was at SLAC. Here synchrotron light (in our case X-rays) are generated when electrons traveling near the speed of light take a curved path around a storage ring (above left red ring on aerial shot of SLAC). The particles blasting around the storage ring emit electromagnetic light in X-ray through infrared wavelengths. The resulting light beam has characteristics that make it ideal for revealing the intricate architecture and composition of many kinds of matter—in our case fossils!

See Bergmann et al 2010 in PNAS for more gorgeous images!

The elemental composition of fossils and the matrix in which they sit can be spatially resolved to ridiculous levels of accuracy here at SLAC. Our team works closely with Dr Uwe Bergman (no less than Deputy Director of the SLAC facility) who helps our team recover these delicate chemical fossils from past eons. Lest we not forget, we are a bag of chemistry...at SLAC, we can start to unpick the remnants of this chemistry that has survived through the sands (muds and limestones) of time.

Synchrotron sheds light on 150 million year old feather biomolecules!

Fortunately for palaeontology (and also the oil industry) the organic building blocks of life can sometimes be stubborn. They do not like breaking down. One such major group of molecules that form the backbone of many organic molecules, goes by the name of functional groups.These groups of atoms are responsible for much of the reactivity of a given molecule as it plays its part in the processes of life. It is these potential 'biomarkers' from deep time that we are so interested in hunting down and mapping in fossils. In my next blog we will take closer look at these chemical flight-recorders...with both x-rays and infrared light. To do this, we will enter the inorganic and organic world of my good colleagues Dr Roy Wogelius and Dr Bart van Dongen from the University of Manchester.

Teasing organic molecules from fossils

This last couple of weeks have been a tad busy...just for a change. A series of papers to complete, review and submit, coupled with meetings at the University of Manchester, entailing a rapid hop over the Atlantic (and yes, you all know how much I 'love' flying). Today, once again, I am sat back in my office at the University of Pennsylvania, watching my 2nd Mac start to splutter as it renders a 3D volume of a T. rex brain case from a micro CT data...as you do. I think I might just have pushed the poor machine a little too far this time, as its been nearly two hours since it started rendering the said volume and its still not responding. This is why I have two Mac's. One to continue working upon, while the other works by itself...slowly, so slow...it has a morning shadow by the time it is done thinking about a problem. That said, it works, but you need patience!

While my 2nd Mac is stumbling its way through thousands of T. rex brain-case slice data, my other is being a little more organic. I have been burying myself into the fun world of organic geochemistry... please keep reading! As if it wasn't for the organic chemistry popping away inside of you, you would not be reading this. However, I have to ask, Why subject myself to such wondrous delights? Its quite simply the only way I can continue to work with my colleagues Dr Roy Wogelius and Dr Bart van Dongen (both at the University of Manchester). They have both been giving me a crash course, these past four years, on the organic and inorganic phases of life...a balance that exists now and into deep time. It seems that if I really want to get to grips with my fossils, I have to know my hopanoids from my geo-hopanes (I assure you that these are not medical conditions associated with digging dinosaurs) and also my FTIR from my Py-GCMS....not to mention your MALDI-TOF (now I'm sure that one should be a cocktail?).

Bart van Dongen hard at work with his Py-GCMS samples!

Over the next few weeks I shall start sticking some of our latest results on these pages, as thankfully we got another paper accepted on soft tissue preservation today...hurrah! Each paper published in a journal is a big step forward for our group, given the techniques we use are quite new to the field of palaeontology, making the review process long in some circumstances. With this in mind, I thought I might dare drag one and all into the fun world of methods, machinery and chemistry that orbits on planet organic...I might even drag vital life processes into the debate, such as fermentation..to help ease the transition into this tricky field. More importantly, you will soon see that fossils are organic mines that we are only just learning how to excavate. I would never have believed that when I was a 7 year old plucking my first fossil from the ground, that I would one day be as interested in the chemistry of the said lump.

Jurassic CSI

Early last year I completed filming a new series for the National Geographic Channel. The fruits of that labour are starting to appear on TV screens around the globe. This series is not just about palaeontology…although dinosaurs are clearly an important theme. The series explores many new techniques in the earth,  physical and biological sciences, from proteomics to particles physics, and from locomotion to geochemistry. The series would not have been possible without the support and collaboration of many scientists at the University of Manchester, but especially Roy Wogelius (SEAES), David Hodgetts (SEAES), Bill Sellers (FLS), Paul Mummery (Materials), Chris Martin (Materials),  Phil Withers (Materials), Adam McMahon (Wolfson Molecular Imaging Centre), Terry Brown (MIB), Alan Crossman (FLS), Jon Codd (FLS), Mark Ferguson (FLS), Matthew Cobb (FLS), Lee Margetts (Research Computing Services) and the staff of the Manchester Museum.

The series will be transmitted in the UK from February 3rd (National Geographic Channel Wild), then in Canada, France, Russia, Turkey, Australia, New Zealand, Japan, Asia (distributed through Taiwan Nat Geo), Spain, Portugal, Italy, Germany and South America National Geographic.

If you want to learn more about the series, click on the links below, as this will take you to the National Geographic Channel web pages for the UK launch of the Jurassic CSI series.

http://natgeotv.com/uk/jurassic-csi

 A large number of video clips have also been placed on the website:

http://natgeotv.com/uk/jurassic-csi/videos

My apologies for the lack of postings this past week, but research, teaching and writing have kept me more than busy. Tonight was a late night again, as Dr David B. Weishampel  from John Hopkins University,  came to Penn and gave a stunning talk on 'Transylvanian dwarf dinosaurs'...great title and even better lecture!

Tasmanian bouncers and egg-layers!

Our drive into the Tasman bush was almost as exciting on-road, as it was 'nearly off-road'...It seems that the accepted local driving technique on dirt-roads with many blind corners involves speed, lack of breaking, expletives, fist-waving and juggling of mobile phone...well, that's what many locals were trying to teach me via positive reinforcement. Each time a tell-tale plume of dust appeared ahead or behind us, I prepared myself for the spray of dirt, gravel and expletives.  Given I was nominated driver, I should have taken photos of the said driving, as I am sure photography could be added to the multitasking ability of Tasman road etiquette. One thing is for certain, the large number of road-kill at the side of every by-way was almost certainly a function of the Taman dirt-road driving code...or lack of one!

A Kangaroo watches us from a safe distance...away from the road!

As we headed north on the island to Mount William National Park, the roads became very narrow, this possibly gave the local wildlife a chance of getting across alive. This was not due to cars slowing due to the narrower, twisting roads, more to do with the animals having less ground to cover as they dash in front of oncoming vehicles...some, I noted on occasion, on the wrong side of the road (vehicles that is!). As we entered the Park we turned off the main dirt road towards the Eddystone Lighthouse, where a campsite was situated drawing many vehicles to this remote part of Tasmania. Off the 'main' dirt road, we slowed our pace to a crawl...in the vain hope we might see local wildlife...alive! We had been saddened by the sheer body count on the road, but slightly heartened by the fact that Tasmanian Devils would get a free meal...albeit the ultimate in fast food, else they too might join their departed meal.

A dark shape at the foot of the tree moved...

Looking for beasties in the Tasman bush initially reminded me of hoping to spy a Kiwi in New Zealand...you know they are there, but you do not stand in a chance of seeing one. Frustrating. Tasmania is different. If you stand still and remain quiet for a few minutes, the bush soon delivers up a bouncing pouched wallaby or suchlike. However, hiding in the shadows near our road was something that none of us expected to see...a monotreme! There are only two groups of monotreme left in the world, found both in Australia and New Guinea. They include the bizzarre egg-laying mammals, the platypus and echidnas, that are essentially like us mammals, bar the egg thing. They have an interesting evolutionary history, in so far it is very poorly known, with a few fossils from Australia in the Cretaceous. These Cretaceous fossil monotremes indicate this group radiated at least 70-80 million years ago...but surely there has to be earlier fossils? Alas, none have been found to-date.

We stopped the car and slowly approached the base of the tree and were greeted by a site we really did not expect. A ball of fur, spines and the pointiest nose you could ever imagine, perched on such a round animal. It was as if a golf tee had stuck itself to a golfball...a spiky golfball. This was our first and possibly last siting of an echidna. Often called the 'spiny anteater' this small spiny ball also supplements its diet with worms, insects, termites and am sure anything the right size that crawls within range of its long sensing nose.

Molecular studies of both the platypus and echidna suggest they share a common water-living ancestor, some 30-50 million years ago. Leaving a watery habitat at this time would have been a brave leap for such a group, given marsupials ruled the Earth...well Australia. Many pouched beasties would have been looking for similar ecological niches to occupy and share with the early echidnas, but it seems they managed to eek-out an existence in the face of such bouncy competition. It has been suggested that the echidnas egg-laying adaptation provided them the edge over the marsupial reproductive strategy. 

After a few minutes of watching the echidna, we all returned to the car with broad grins. Knowing that we had all had a close-encounter of a spiky, monotreme kind. Simply stunning. The echidna waddled-off about his or her business...am not sure how you might determine the sex an echidna?

As we drove further into the Park, the kangaroos and wallabys became less weary of our car...possibly because they did not recognise it as a car, given we were driving slowly, engine not screaming, and horn not blowing. As I spied a wallaby almost outside our car, I stopped. With a hint of guilt, we all snapped photographs of the shy herbivore, remembering the 'Wallaby Jerky' I had eaten in Sydney airport a few days earlier.

While many of us happily eat cow, chicken and pig...(ah, the memory of the CCP burger in South Dakota last year...yes, a CowChikenPig burger!), the thought of eating marsupial was initially odd. But I have also to admit, the night before we had all tried wallaby sausages and they were good! Gives a whole new twist to, 'One mans meat is another mans marsupial'....

For many years I have been fascinated by wallabys, this in part was due to a paper by McNeil Alexander on the elastic recoil he measured in the hind limbs of these hopping macropods (literally 'big-foot'). If it wasn't for the fact that they hopped, when seen at a distance...a long distance...you could be forgiven for thinking they have an almost dinosaurian body outline...until they move. However, as Bill Sellers, colleagues and I suggested in a paper last year...hopping might well have been in the locomotor repertoire of some bipedal dinosaurs! Even I, as a child, have been driven to hopping...usually in a school race! I'm not suggesting that dinosaurs hopped around the Mesozoic, just that they were capable of a hop, if the mood took them.

However, the limb and pelvic adaptations of macropods places them in a hopping league all of their own, with some of the larger kangaroos being able to reach speeds upwards of 40 miles per hour for the 200 pound red kangaroo (Macrpus rufus). This bounder can also leap up to 25 feet in a singe hop, but also clear a 10 foot fence...that's accomplished hopping!

By the end of our long day in the north west edge of Tasmania we headed back to Hobart and to the our hosts Andrea and James. Tomorrow, we had work to do...of a bunny variety. Alas, I cannot share this work with you, as its part of a research program of a colleague at Penn. However, I shall pick-up my Tasman tale with a brief look at some very, very, very old fossil wood!