Beauty in a speck of dust


Phosphatized pre-Cambrian embryos are cool. It’s amazing that they’ve been preserved at all, and they are spectacularly gorgeous. We can learn about the evolution of development from their superficial appearance, but what we really want to do is poke around their interiors and analyze them cell by cell, something that has been hard to do without destroying them in the process. Until now.

A report in Nature (and a too short mention on a researcher’s web page) describes the application of synchrotron X-ray tomographic microscopy (SRXTM) to these fossilized embryos to resolve their internal structure. It’s a powerful tool, and it’s generating some beautiful images.

The technique basically involves blasting the sample with X-rays and reconstructing the three-dimensional structure on a computer. It’s something I wish we could do with live embryos, but I suspect they have to be mineralized before they can survive the procedure…but that means that these images are often better than anything I’ve seen in embryos that haven’t been dead for over a half billion years.

Here are some reconstructions of blastula stage embryos. You can trace the outlines of individual blastomeres (the cells that make up the embryo) and follow the stacks of cells from the center to the periphery.

(click for larger image)

Divisions between adjacent blastomeres variably preserved on the surface and within. a, b, Museum of Earth Science, Institute of Geology, Chinese Academy of Geological Sciences (MESIG) 20061. Divisions between some, but not all, blastomeres are preserved internally. c, d, MESIG 20062. Divisions between all, or nearly all, blastomeres are preserved to their full extent; the orange and yellow structures are renderings of the morphology of a column of blastomeres. e?g, Geological Museum of Peking University (GMPKU) 2204. Divisions between blastomeres are generally not preserved, and instead the core of the embryo is characterized by the centrifugal addition of diagenetic crust layers (easily distinguished from edge artefacts through their absence from some of the objects seen in the slices); orange structure represents a rendering of one of the cavities within the diagenetic infilling.

Greater detail can also be used to resolve phylogenetic disputes. This is an example of Markuelia. What is Markuelia? It’s a small wormlike creature that has been proposed to be a member of a group called the Scalidorpha, which includes some fairly obscure marine worms, like the priapulids. It’s also been suggested that it might properly belong to the Nematoidea, which includes the nematode worms. One feature that distinguishes the two groups is the arrangement of spines in the mouth and pharynx, both in number and their orientation. Scalidophorans can invert their mouth parts to capture prey—if you remember those wormlike monsters on the recent remake of King Kong, you’ll have an idea of what that’s like.

With the SRXTM, they can see all the spikes and spines and fangy bits of the fossil’s mouthparts, as you can see in this series of scans, where the colored parts are the oral and pharyngeal spines.

(click for larger image)

a?f, GMPKU 2205. Whole-mount tomographic reconstruction of Markuelia hunanensis from the Upper Cambrian of Wangcun, Hunan, Southern China. b?f are rotated 90°; from a. a and b show the whole reconstruction, with all scalids. c?f, 25 circumpharyngeal scalids arranged in rings surrounding the mouth cone (f). 25 scalids are shown in the first three rings (c), 16 scalids are shown in the first two rings (d), and 8 scalids are shown in the inner first circumoral ring (e). g, h, GMPKU2011. Tomographic reconstruction of posterior spines and a section revealing the terminal end of the digestive tract of M. hunanensis. i, j, Swedish Museum of Natural History (SMNH) X2240. Markuelia secunda from the basal part of the Pestrotsvet Formation at Dvortsy, Aldan River, Siberia. Scanning electron micrograph (i) shows four terminal spines arranged in two pairs, while the tomographic reconstruction (j) shows a third, obscured, pair.

It’s toothy like a scalidiophoran. That’s an amazing level of detail.

I think we can look forward to many more images like these—this is going to be a very popular tool for analyzing microfossils.

More can be found at Philip Donoghue’s website.

Donoghue PCJ, Bengtson S, Dong X-p, Gostling NJ, Huldtgren T, Cunningham JA, Yin C, Yue Z, Peng F, Stampanoni M (2006) Synchtrotron X-ray tomographic microscopy of fossil embryos. Nature 442:680-683.


  1. #1 quork
    August 10, 2006

    The technique basically involves blasting the sample with X-rays and reconstructing the three-dimensional structure on a computer. It’s something I wish we could do with live embryos, but I suspect they have to be mineralized before they can survive the procedure

    No, they would not survive the procedure. Moreover, you probably couldn’t complete the image before the embryo disintegrated.

    Sample damage is just one limitation. Another is low contrast. Carbon, nitrogen and oxygen all look pretty much the same to X-rays. You could try heavy metal fixing agents, a la electron microscopy, but then you start to get further away from the live cell you were interested in in the first place.

  2. #2 rrt
    August 10, 2006

    Is there a snowball’s chance in hell that internal cellular structure is preserved, and visible via these techniques?

    Re: the King Kong worms: The most disturbing scene in the movie for me, and one of the most jibblies-inducing scenes I’ve seen in many years.

  3. #3 DragonScholar
    August 10, 2006

    Extremely impressive – takes me back to my embryology class. Kudos to the people who worked on this – they’re serious heroes of science.

    I’d wonder too how many phosphatized embryos are stored out there – since they sound rare, perhaps not much. But I’d suspect it’s time for those that have them to start digging them up . . .

  4. #4 quork
    August 10, 2006

    Is there a snowball’s chance in hell that internal cellular structure is preserved, and visible via these techniques?

    This being a Nature article, I can’t find much of anything on their methodology. Their technical reference is:
    High resolution X-ray detector for synchrotron-based microtomography
    Marco Stampanoni, Gunther Borchert, Peter Wyss, Rafael Abela, Bruce Patterson, Steven Hunt, Detlef Vermeulen and Peter Rüegsegger
    Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment
    Volume 491, Issues 1-2 , 21 September 2002, Pages 291-301

    In the accompanying Nature News and Views,
    Microscopy: Nanotomography comes of age
    David Attwood
    Nature 442, 642-643(10 August 2006) | doi:10.1038/442642b; Published online 9 August 2006,
    it says:

    Writing in Applied Physics Letters, Yin and colleagues report an X-ray microscopy technique of broad potential for three-dimensional imaging in the physical and life sciences. By tuning high-energy X-rays, the authors manipulate the contributions of specific chemical elements to a series of two-dimensional images. They then use tomographic methods to combine images taken at different incident X-ray angles, allowing internal structures and — given sufficient spectral resolution — chemical bondings to be discerned with a spatial resolution of around 60 nanometres.

    Here’s the referenced article:
    Energy-tunable transmission x-ray microscope for differential contrast imaging with near 60 nm resolution tomography
    Gung-Chian Yin,
    Appl. Phys. Lett. 88, 241115 (12 June 2006)

    I haven’t followed the chain of publications to the end yet, but the resolution is probably limited by the size of the X-ray beam, in which case it will almost certainly improve with future technological advances.

  5. #5 Tlazolteotl
    August 10, 2006

    synchrotron X-ray tomographic microscopy

    I was working my way through college as a clerk in a local hospital x-ray department just as ultrasound and CT started coming into use, and all I can say to this is “wow.”

  6. #6 Bruce
    August 11, 2006

    Dayum; that is amazing stuff! Look closely enough at the world and the idea of a designer (G*d) just seems so unnecessary. Photos like these should be in every elementary school classroom in the nation.

    (I knew those King King worms had to be real somewhere!)

  7. #7 Phil Donoghue
    August 13, 2006

    Hi, I am one of the authors on this paper – thanks for the kind comments. I just wanted to direct those guys interested in the technique to the supplementary data we provided with the paper, available directly (and freely) from the Nature website.


    It includes a textfile on the method (still very brief) but also a whole load of movies of the scan slices that we based our reconstructions on.