The chemical ghost of a 120 million year-old bird

July 9, 2012 • 2:20 pm

by Matthew Cobb

I spent Friday-Sunday last week at the Royal Society Summer Exhibition, helping out some colleagues from the Manchester University Geochemistry & Paleontology Research Group as they explained their research to the public. I had such fun, and the stuff we were talking about was so interesting. What follows is pretty much the pitch I gave to the public, as someone who wasn’t directly involved in the research. Two WEIT readers came up  who had recently graduated from Queen Mary, London – I didn’t catch their names, but hi!

The centre-piece of our display was a 120 MY old fossil of Confuciusornis sanctus, a basal bird from China – it is the earliest known bird with a beak. About the size of a pigeon, it had long twin tail-feathers strongly suggestive of sexual selection. This bird was one of a flock that was caught in a volcanic explosion one Tuesday afternoon (I made that bit up) and ended up fossilised at the bottom of a lake. The fossil itself is pretty neat, with clear impressions of feathers, bones and soft tissues (see image A below):

Fossil Confuciusornis sanctus; A: optical image B: False-colour signals from X-ray fluoroescence; Green = zinc; blue = calcium; red = copper (Wogelius et al., 2011)

As a biologist, I’d be happy with the fossil, but my colleagues Roy Wogelius and Phil Manning from Manchester Earth & Environmental Sciences, together with Uwe Bergmann from Stanford and a host of other folk, decided to use a technique they had previously employed on an Archaeopteryx fossil (Bergmann et al., 2010). They put the fossil at the sharp end of the Stanford synchotron and fired a concentrated X-ray beam at the fossil. In response to this procedure, the atoms of the different elements require different energies to fluoresce, so an ‘elemental map’ of the fossil can be built up.

Figure B above shows the signals for three elements: zinc (= green), calcium (= blue) and copper (red). The zinc is present in background levels in the matrix and shows no specific information about the fossil; calcium is present in the bones and beak, and only in the bones and beak. On the one hand, this is trivial (where else would it be?) and on the other it is amazing – it shows that the fossil is not simply a physical impression, there are also chemical traces that are trapped in the rock: atoms of calcium that were once in the bird’s bones.

The red signal of copper is the most audacious to interpret. You can see that it is on the outside of the animal, primarily in the feathers (look at the intense staining in the upper body). However, not all the feathers show this staining – look at the large wing feathers on the bottom left and bottom right of the fossil – they do not show any copper. So the distribution of copper in the feathers is non-random.

Roy and the rest of the team were able to show that this copper is definitely organic, and shows the coordination chemistry that is typical of eumelanin (I am skipping over several complicated stages of chemistry here – details in the references). This would suggest that the distribution of copper could be a biomarker for the presence/absence of melanin in the tissues of the living bird.

To test their hypothesis, they took various feathers and control samples, modern and fossil, and subjected them to the same X-ray fluoresence. The results strongly support their view (I find modern feathers D and E and their X-ray equivalents L and M particularly convincing):

A to G) optical images and (H to O) false-color images of: [(A) and (H)] Green River fossil feather; [(B), (I), and (J)] Green River fossil feather and fish; [(C) and (K)] G. yumenensis fossil feather; [(D) and (L)] eagle feather; [(E) and (M)] blue jay feather; [(F) and (N)] Hakel fossil squid; [(G) and (O)] sectioned extant squid. For H & J: red, Cu; green, Ca; and blue, Fe. For K: red, Cu; and green, Ca. For the remaining images, red, Cu. (Wogelius et al. (2011)
As a result, my colleagues interpreted the black/white distribution of colour thus:

This is cool because it shows the colour (or at least, the black and white distribution) of C. sanctus. Even more interestingly, along with the rest of their work, it clearly shows that fossils are not simply physical imprints, but also chemical traces that, with the right technology, can be interpreted in biological terms: we can work out the biochemistry of cells in an animal that died 120 million years ago. However, it isn’t straightforward: interpreting the distribution of copper was possible because they could demonstrate that it was a good biomarker for eumelanin. The distribution of other elements is not so easy to interpret – the biology is going to be as complicated as the particle physics and analytical chemistry.

There are other techniques for determining colour in fossils – in the same issue of Science that Roy and his colleagues published their findings, Ryan McKellar examined a load of late cretaceous dinosaur and bird feathers that had been trapped in amber. And in 2010 two papers on other fossils of primitive birds and dinosaurs using scanning electron microscopy suggested that the cellular structures involved in pigmentation – melanosomes – could be reliably detected in some specimens (Li et al, 2010; Zhang et al., 2010). The advantage of the technique used by my colleagues is that it relies less upon exceptional preservation, and it gives a whole-organism view. The trick, however, will be to find reliable interpretations of the elemental distribution.

To find out more about the technique, including some examples of its use on archaeological artifacts, including a ‘lost’ score by Cherubini, see Bergmann (2012).

To accompany the exhibition, Phil Manning made an e-book for the iPad, called “Chemical Ghosts”. This is available *free* from the iBook store. He also made an excellent free app, again for the iPad and called “Chemical Ghosts” (there are no Android versions I’m afraid, and they don’t work on the iPhone). At the end of the app, the camera starts up on your iPad (so it doesn’t work if, like me, you have an iPad 1 with no camera…). If you present this image to the camera (probably best to print it out), and get it in focus, you will be amazed what happens. Turn the image to one side and another – this was one of the best bits of the exhibit! People were absolutely amazed. Honest!

UPDATE: Here’s an image of what you see with an iPad with a camera – people in the comments have been asking. This was taken by Phil Manning himself. It’s a 3-D “augmented reality” rendering of the bird. You can move it in three dimensions as you move the cartoon of the bird. It’s really rather impressive (and better than this 2-d snapshot!). Note the realistic shadow!

Augmented reality Confuciusornis sanctus


There’s a website at the Royal Society about the exhibit, and Phil Manning has his own dinosaur blog.

References (links are only to abstracts I’m afraid, unless you have personal or institutional access):

U. Bergmann, R. W. Morton, P. L. Manning, W. I. Sellers, S. Farrar, K. G. Huntley, R. A. Wogelius, and P. Larson (2010) Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging. PNAS 107:9060-9065

Uwe Bergmann, Philip L. Manning & Roy A Wogelius (2012) Chemical mapping of paleontological and archeological artifacts with synchotron X-rays. Annual Review of Analytical Chemistry 5:361-389.

Quanguo Li, Ke-Qin Gao, Jakob Vinther, Matthew D. Shawkey, Julia A. Clarke, Liliana D’Alba, Qingjin Meng, Derek E. G. Briggs and Richard O. Prum (2010) Plumage color patterns of an extinct dinosaur. Science 327:1369-1372

Ryan C. McKellar, Brian D. E. Chatterton, Alexander P. Wolfe, Philip J. Currie (2011) A diverse assemblage of late Cretaceous dinosaur and bird reathers from Canadian amber. Science 333:1619-1622

R. A. Wogelius, P. L. Manning, H. E. Barden, N. P. Edwards, S. M. Webb, W. I. Sellers, K. G. Taylor, P. L. Larson, P. Dodson, H. You, L. Da-qing, U. Bergmann (2011) Trace metals as biomarkers for eumelanin pigment in the fossil record. Science 333:1622-1626.

Fucheng Zhang, Stuart L. Kearns, Patrick J. Orr, Michael J. Benton, Zhonghe Zhou, Diane Johnson, Xing Xu & Xiaolin Wang (2010)Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature 463:1075-1078

37 thoughts on “The chemical ghost of a 120 million year-old bird

    1. Let me know what you think of the surprise at the end of the app (even better – take a picture of what you see with the camera and send it to us!)

    2. Since I’ll never have an iPad, I’m hoping someone will post the details of the surprise, too. 🙂

  1. 1. Did the bird really have “feet” on its wings? I’ve heard of clawed wings (the claws being more like modified feathers) but movable feet would give the bird an entirely different way of moving (climbing?) than any modern bird.

    2. It would be neat to see the imaging technique used with modern feathers that have contrasting light/dark bars, such as the caracara or the black and white woodpeckers (stark black and white stripes) and wild turkey (white/dark gray). The blue jay feather is essentially black with a white tip (the blue is structural, not pigment).

    1. Primitively, with birds being descended from a reptilian origin, one would expect some birds to have clawed manus (“hand”) and pes (“foot”). Clearly modern birds generally still have a clawed pes. Rare modern birds, the Hoatzin specifically, and possibly others in the egg or as occasional atavisms, also have a partly clawed manus. So, seeing claws on the manus of Jurassic to Early Cretaceous birds is no surprise. These claws are digits, like your digits or whale’s flippers ; not modified feathers (which are skin features – essentially scales).
      I don’t recognise the names of any of the birds you mention, so I guess they’re non-British species. So that I guess is why Manning et al didn’t use them – no materials readily available. Otherwise, the illustrations show that the resolution of the technique is around a millimetre for modern feathers, so I presume it would work adequately for any modern bird with such a colour spacing in individual feathers. Unfortunately, my only book of British birds depicts them with their feathers “on”, not “off”, so how much of their patterning is due to changes in a particular feather, and how much to differently coloured feathers, I can’t say. There are certainly British birds with patterned feathers (OK, I’m thinking of introduced birds actually, not that it really matters), but they’re shades of light and dark brown, which may not be high-enough contrast. I’m not a twitcher to know more.

      1. The blue in a blue jay (and as far as we know all blue feathers in all birds) is indeed a structural color, but in fact it relies on a melanin backstop in order to make that color work. An albino blue jay is white, even though it still has the same feather structure as a normal blue jay. It lacks only the melanin.

        There are also several birds that have claws on their wings as adults. Even chickens do, fairly frequently. What they don’t have, usually is free digits like Archaeopteryx, which certainly could have used them to climb trees.

  2. Edward Feser would prattle about how God directed the process for that bird,ignoring science’s finding that’s a no,no as the Coyne argument notes.
    That quack joins my pack of theological fools for Christ!
    Tom Clark, what would you say to Feser about his divine teleology? Would you endorse the Coyne mechanistic argument [ the Coyne-Mayr-Lamberth teleonomic argument].
    Feser thinks we have free will. I maintain that we have determined volition.
    Ornithologists can rattle off many transitions for birds as primatologists for our own lineage.
    How might we get creationists to get over their God-addition? Are their determinants that we could use? Creationists here in the wide sense as all theists as evolution theism is just an oxymoronic obscurantism! See my article of May twenty-fourth that skewers God in general and Yahweh in particular. has many articles against the God-addiction and for naturalism.
    And you and other naturalists might post at any of them,even correcting my own articles and posts!

    1. “How might we get creationists to get over their God-addiction?”

      And that, my friend, is the $64,000 question. I haven’t a clue what the answer is, but suspect it lies in psychology. Any academics reading would do well to suggest to their colleagues in their institution’s psychology department that it would be a worthy project to study creationists belief systems and try to find out just why they are so impermeable to the obvious evidence. Surely to heavens, there’s some method that would crack open their shells and let the light in!

  3. Hi Prof Cobb,

    It was me and my friend Katie who were the Queen Mary people, thanks for a fascinating chat, it was one of the most astonishing things I saw that day, and there was a lot of good stuff; I’m going to have to get an iPad now I suppose after seeing that bit of technological witchcraft.

    We’ve been studying fossils for centuries, X-rays were discovered by the Victorians and we’ve been playing around with particle accelerators for a good long while too, but this technique has only just appeared! Just shows where a bit of interdisciplinary cooperation can get you.

    Presumably it’ll become a fairly standard bit of the palaeontological toolkit (provided you can get your hands on a synchotron) so I suppose we can expect a lot more results like these, and like you said, interpreting the more complex and subtle signatures will be difficult but there’s bound to be meaningful data to be had.

    Great stuff.

  4. So, what, you’re an honourary Brit, now? Spelling “color” incorrectly and whatnot! Thanks for the astonishing information! My jaw literally dropped. Ain’t science grand?!

    1. Umm, the byline says it all – I wrote the article and am guilty of being a Brit, “colour” and all.

      1. Took me a while to remove my large electronic foot from my mouth! I missed the byline, I guess. Anyway, great stuff!

  5. OK, I have posted an update in the post above, so you can see what pops up at the end of the app!

  6. On the one hand, this is trivial (where else would it be?) and on the other it is amazing – it shows that the fossil is not simply a physical impression, there are also chemical traces that are trapped in the rock: atoms of calcium that were once in the bird’s bones.

    Little correction here, because this is a common misconception. We have always known these fossils (and the bulk of other vertebrate fossils) to be not just impressions but actual bones. (In some fossils, the feathers are just, or chiefly, impressions.) The calcium wasn’t “once in the bird’s bones”; it’s still there, since the bone itself is still there. Living bone is a complex of protein and the mineral hydroxyapatite, which contains calcium. In fossils, the protein is usually (again, mostly) decayed and/or gone. But the hydroxyapatite is still there, untransformed. As is the case in Confuciusornis.

  7. His supposed refutation of the logical argument from evil..Fr. Meslier’s the problem of Heaven refutes all defenses and theogicies!That argument is at the top of Fr. Griggs, with more in later posts. And there also see my own article after the one about Aquinas’ five failed ways.

  8. Uncle Fred! We always wondered what happened to him – he just went out for a quart of milk —

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