The Rabbit Whole

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3D Printing the Long Term Carbon Cycle

Jamie Perrelet
Schumacher College
2013

Introduction

Whilst humanity stands teetering over the precipice of extinction, it stares out over a vast ocean of possibility. Emerging technologies are offering novel insights into the greatest challenges of the twenty first century and although there are no quick fixes, a new age amidst a world of shifting tides is dawning. We are presently passing through a doorway into the next industrial revolution; a rite of passage into a time of decentralised manufacturing, energy production and communications. As rapid prototyping machines become household items, the vision of a solar powered 3D printer, capable of producing a virtually unlimited range of items (including versions of itself), using directly recyclable materials, will soon be a reality. It is difficult to even begin to grasp at the implications of such a technology. What consequences will it have for our relationship with the planet?

Among the growing applications of 3D printing is the capability to use physically printed models as innovative and transformative learning tools, which can help bring our understanding of the world to life. This work is intended to be an introductory exploration of this technology in the context of education and in particular, the long term carbon cycle of the planet.

Education & 3D Printing

The ability to print three dimensional computer models has been possible since the 1980’s however recent years have seen an upsurge in the development of the technology. It is now readily feasible to accurately 3D print virtually any shape in a growing range of materials including plastic, metal and sandstone, among others. Some have described the infant stages of this technology as the birth of the next industrial revolution, of which we have only begun to scratch the surface of the implications.

Across orders of scale, from molecular interactions to the structure of the cosmos; science has bestowed humanity with the ability to discover that which is beyond direct sensorial perception. Whilst computer generated graphics and animations have helped to bridge the vast gap between theory and experience, these approaches remain confined to the two dimensional screen. Many of the structures and geometries described by modern science are far too complex to be crafted into models using classical means, however 3D printers have a practically unlimited capacity to replicate intricacy. 3D printing technologies offer the opportunity to transfigure the abstract diagrams, geometries and images of science into tactile and tangible experiences. Given the rapidly decreasing cost of these technologies, this vision is not to be found in the distant future; rather it is the budding reality of today.

The Long Term Carbon Cycle

Granite’s life begins several kilometres below continental margins, where basalt magma and water are heated under huge pressures, crystallising into granite. The newly birthed granite is gradually uplifted to the surface through mountain building processes and as the overlying rock is eroded, granite formations are progressively revealed. Exposed to the elements, the granite is subject to erosion through chemical weathering. Atmospheric moisture and carbon dioxide combine to produce carbonic acid, a molecule that easily dissociates into a bicarbonate ion and a hydrogen ion, a single proton. The positively charged hydrogen nuclei pass through the granite’s crystalline lattice, neutralising the electrical bonds between oxygen and silicon ions inside the rock. Calcium ions are liberated as the granite gradually disintegrates, which react with atmospheric carbon to form calcium bicarbonate, a soluble form of limestone. Incredibly, this weathering is intimately entangled with the organic life that lives on the surface of the granite; as lichen, algae and plant roots can speed up the rate of erosion by up to a thousand fold. The process removes carbon from the atmosphere and therefore has the consequence of causing a net cooling effect of the planet.

eq1

Dissolved in rainwater, the released calcium and carbon molecules permeate the soil, flushing the remaining granite minerals such as silicon and aluminium, along with it. Flowing over land and into rivers, the minerals are carried out into the ocean, where a miraculous metamorphosis takes place. Crustaceans, coral and marine algae precipitate the calcium bicarbonate into their chalky shells through a process called carbonate deposition. Although this releases carbon into the atmosphere, half of the carbon atoms remain locked up in the form of calcium bicarbonate. Further, as algae are photosynthetic beings, they naturally absorb an amount of this liberated carbon through photosynthesis.

eq2

One of the most prolific uptakes of aquatic calcium is by a family of microscopic phytoplankton called coccolithophores, Latin for ‘carriers of little stone berries’. Only microns in diameter, these single celled beings skilfully encase themselves in an intricate and ornate mosaic of chalk plates, called coccoliths. Oxygen and silica released from the weathered granite, are sequestered by another group of phytoplankton called diatoms, which use it to craft delicately constructed glassy shells, called frustules.

cocco-diatom

A sample of four different species of coccolithophore (left) and diatoms (right). Source: Nature.

As coccolithophores, diatoms and other marine algae die, their microscopic skeletons sink in a perpetual shower of calcites and silicates, settling on the bottom of the ocean. They are so plentiful in their numbers that coccoliths are able to accumulate in vast sedimentary repositories on the seabed; becoming compressed into solid chalk over geological time. The silica frustules of diatoms are crushed into nodules of flint within the chalk and under certain conditions these chalk slabs can be uplifted above sea level, as exemplified by the white cliffs of Dover. Such exposed chalk deposits are prone to erosion and overtime the deposited carbon and calcium invariably makes its way back into the ocean through carbonate weathering; the reverse of carbonate disposition.

Conversely, when oceanic crust collides with a continental plate it is subducted underneath the continent, carrying sediments with it. Under increasing temperature and pressure with depth, the sedimentary chalk and limestone melt into new newly formed granite through the process of carbonate metamorphism; replenishing the granite eroded by weathering and thereby completing the cycle. Carbon stored in the chalk is released as carbon dioxide gas which rises up from deep under the continental margins and is liberated through dramatic volcanic events. The released carbon offsets that which is absorbed through weathering, regulating the atmospheric concentration of carbon and with it the global temperature.

eq3

The long term carbon cycle is a remarkable story, it illustrates a phenomenal synthesis between the earth’s crust, mantle, oceans, atmosphere and the inhabiting biota. The most significant challenge in communicating this epic is a question of magnitude; both in time and in scale. The cycle evolves over millions of years and encompasses orders of scale extending between individual molecular interactions and microscopic phytoplankton and colossal plate tectonics.

Deep ecologist, Stephan Harding, offers a novel and spirited way of bringing the long term carbon cycle into the context of the feeling body. In his book, Animate Earth, Harding describes a kind of geological mediation titled ‘Breathing Chalk and Granite’, which merges the ancient process of carbon sequestration and emission with the cyclic passage of ones breathe. Sitting comfortably and breathing naturally, the participant is asked to envision the entire carbon journey, holding in one hand a piece of granite and in the other a piece chalk. With each inhale, carbon dioxide is visualised being drawn out of the atmosphere and fixed into the eroding granite, where it is flushed out into the ocean. Coccolithophores and diatoms uptake the calcium and silicon based molecules into their elaborate shells, settling on the seabed over geological time. Crushed into chalk and flint and subducted along continental margins, each exhale is felt as an upsurge of carbon dioxide from deep in the Earth’s crust in a ground shaking volcanic crescendo.

Modelling Phytoplankton

The focus of this enquiry is to further elaborate on the richness of the story; using the latest technology to bring these metamorphic transformations to life. The intricate structures of phytoplankton are so elegantly crafted that they would have no difficulty being exhibited in a fine art gallery. Like delicate Victorian lace, coccolithophores adorn themselves in a sophisticated web of calcite beauty, while the almost science fiction designs of the silicate diatoms appear stylised to reflect the geometry of ultramodern architecture. Perhaps it is no coincide that the essential ingredient in bone china is calcium and that of the modern computer is silicon.

With computer assisted design and 3D printing technology it is possible to scale these otherwise microscopic beings to human proportions, allowing their perplexing beauty to be revealed in the palm of the hand. Emiliana huxleyi, the most common species of coccolithophore and diatom, Campylodiscus hibernicus, were chosen for modelling, both scaled to approximately 10,000 their original size.

The Design Process

The modelling process of the Emiliana huxleyi coccolithophore starts with the use of two computer programs; TopMod and Wings3D, both specialised in the fabrication of complex manifold geometries. The desired result is the construction of a single coccolith plate, which can be replicated to produce the complete structure of the coccolithophore. Graphical images of the following steps are shown on plates A and B in the appendix. The process begins by drawing a pair of elliptical toroids; a thicker one for the inner edifice and a thinner one for the outer ring. Next, a series of extrusions are made from the inner toroid, which are sequentially bridged to the outer ring, creating an array of 36 linking arms between the two toroids. Finally a geometry was shaped in the centre of the coccolith, from which a second array of arms were constructed to fashion the inner details.

The finished coccolith is then imported into 3D Studio Max, where a template sphere is created to guide the assembly of the coccolithophore. Each coccolith plate is given a variation in size and assigned an amount of random distortion, before being added to the surface of the sphere. Each plate must be positioned to provide enough overlap to ensure that the model will be structurally sound when it is 3D printed. Finally a global set of filters are applied to the model including smoothing, spherical adjustments and thickness control.

cocco2

Rendering of the completed Emiliana Huxleyi model.

The creation of the Campylodiscus hibernicus diatom begins with a hollow cylinder to create the outer case of the creature’s cell wall and inner geometry as the central plate. The perimeter of a circle is split in half and positioned to form the upper rail that wraps the circumference of the frustule. The skeletal lattice of the diatoms complex structure is fashioned with an array of bridging elements running between the upper rail, the main cylinder and the central plate. Finally, a copy the entire model is rotated 90 degrees and reflected to generate the symmetrical lower part of the shell. The diatom is imported into 3D studio Max where it is distorted to generate the necessary hyperbolic curvature, so characteristic of the Campylodiscus hibernicus species. Similarly to the coccolithophore, a set of finishing filters are applied to the diatom for smoothing, tweaking and preparation for the 3D printing process.

diatom

Rendering of the completed Campylodiscus Hibernicus model.

Suggested Guide

These printed objects can be used as conventional demonstration models, however they may evoke a greater sense of meaning in a more intimate context.  The exercise outlined here is inspired by the Goethean approach to knowing; a powerful method of enquiry that allows one to meet the nature of a phenomena in its wholeness.

Sitting comfortably in a clear space, either outside or in, give yourself a few moments to centre. Take a piece of granite and a piece chalk and place them in front of you, either side of the two printed models. Starting with the granite, take it in the palm of your hand and survey the rock from all perspectives, absorbing the various details as you go. Taking note of the granite’s various facets, meet the rock with your enquiry. What textures does it have? How hard is it? What patterns do you see? You may wish to make various sketches. After spending some time with the granite stone, move onto to either one of the phytoplankton models. Do as you did for the granite, this time paying particular attention to the overall structure, allowing yourself to feel the sensations that the geometry reflects in your being. Repeat the process until all four models have been well examined, taking the opportunity to return to any of the objects as needed. Gently closing your eyes, step by step, from granite to chalk, begin to imagine the metamorphic journey of carbon in your mind’s eye. Now, holding a stone in each hand, explore Stephan Harding’s breathing with granite and chalk meditation.

models
Conclusion

Designing and printing your first model is a little like an initiation into a futuristic form of alchemy, where at the click of a button, that which was once confined to a screen’s pixels, is transformed into a physically tractable object. Only time will tell what the future of this technology holds, however it is clear that being able to rapidly fabricate and experience three dimensional models of otherwise distant or abstract scientific discoveries, has huge implications for the way we learn.

The effectiveness of this learning set could be easily enhanced with the addition of any number of extra models, which might include other species of phytoplankton or the representation of the relevant molecular interactions. Furthermore, from the enigmatic orbitals of electron clouds to the manifolds of abstract algebra, there is a practically unlimited scope of possibility to use this technique as a learning tool elsewhere in science.

Finally, as an artist with a passion for form, I feel I have stumbled across an innovative way to connect with the outstanding artistry of the nineteenth century biologist, Ernst Haeckel, who was so devoted to documenting, classify and drawing the intricate world he witnessed through his microscope. Beyond academic study, this research has deepened my relationship with the extraordinarily creative potential of our planet to express herself through enchanted forms of ingenious beauty.

Appendix
coccobuild

Plate A: Constructing the portrait of a Emiliana Huxleyi Coccolithophore.

diatom-build

Plate B: Constructing the portrait of a Campylodiscus Hibernicus Diatom

phytoscene

Plate C: An artistic impression of coccolithophore and diatom life in the open ocean.

21 Comments on 3D Printing the Carbon Cycle

  • Amanda Lea Whitmire says:
    17th March 2017 at 9:56 pm

    These models are fantastic! Have you made the 3D files available for download or for purchase? I’m looking for models of phytoplankton to print for classes and outreach (I’m a librarian at a marine biology research station and I have a 3D printer in the library). Nice work! Cheers.

    Reply

  • jamie says:
    19th March 2017 at 12:16 am

    Hi Amanda. Thank you for your kinds complements – I’m very grateful to get the feedback from someone who is actually in this field of research. Regarding models, I did upload them to shapeways some time ago, however I’m unsure if they’re still there… How about I just send you over the files and you can see how they replicate?.. I’ve found them to be excellent educational tools. Blessings from Devon.

    Reply

    • Bob says:
      2nd April 2018 at 5:29 pm

      Hi Jamie,
      Can you please tell me where I can get the files to reproduce these phytoplankton models on our own 3d printer. They are beautiful! I teach oceanography at the university level and these will come in very handy (pun intended) in the classroom.

      thanks
      Bob.,

      Reply

    • Adriano says:
      16th April 2018 at 12:26 pm

      Hi Jamie,

      I’m looking for stl-files of plankton. We would like to print one (or some) as a gift for my boss, a paleontologist who studies coccolithes and soon will retire. Could you help me with this?

      Thanks in advance.

      Reply

  • jamie says:
    19th March 2017 at 12:50 am

    Sent 🙂

    Reply

  • Line Friis Frederiksen says:
    26th April 2017 at 2:25 pm

    Hi Jamie
    They are just wonderful – the coccolith models!!
    We are producing a danish popular science program telling stories about the danish coastline through time – for our public service tv-station DR. We are in that context making a story on limestone and coccoliths – and have been looking for a good way to show people just how beautiful natures design is, and yours are the only big models, I have come across.
    Would you be willing to send us your 3D-files – then I will try to find a 3D-printer to print them on?
    Kindest regards
    Line

    Reply

  • Carsten Thuesen says:
    28th April 2017 at 12:31 pm

    I am looking for a 3D model (to print, for educational purpose) of a Coccolith, an stumbled upon a link fro the Ultimaker website “https://ultimaker.com/en/community/prints/11571-diatom-frustule”.
    Your models looks fantastic, is it possible to get a file for download for printing? Thanks!

    Reply

  • Julien says:
    26th September 2017 at 6:44 am

    Hey Jamie !

    I’m actually working on a project involving diatoms and i really found your 3D work with those frustule amazing. I was wondering if it was possible to download or purchase the files for printing.

    Thanks !

    Reply

  • Lynn Taylor says:
    11th March 2018 at 8:22 pm

    During Sea Week in NZ (July) I am assisting Science Communication students with an exhibition in the Community Gallery where there will be various free SciArt activities happening. One student’s research is on CO2 + temp effects on Emiliania Huxleyii. It would be incredible to have a 3-d model for people to interact with – could you please let me know the possibility of downloading/accessing your files and cost. Many thanks, Lynn

    Reply

  • Diana says:
    15th April 2018 at 3:47 pm

    Same request than the other ones. Could I download or purchase the 3D model of Emiliana huxleyi for 3D printing for education?
    Thank you!

    Reply

  • Darius Kesean says:
    1st May 2018 at 7:49 pm

    Hi your designs are awesome. I am a scientist and I work specifically with E. huxleyi and would like to 3d print the models you have. It would be great for my talks when I explain to people the ecological importance and just how cool these diatoms/phytoplankton are. So can you please send me the models? Thanks

    Reply

  • Liam Gallagher says:
    27th July 2018 at 12:16 pm

    Jamie,

    I would love to be able to use your file of the E hux. I am advising the Etches Museum in Dorset on the microfossil content of the Kimmeridge Clay at the moment and we need a 3D model of a coccosphere to kick start the outreach content – would you be able to share the file please?

    Reply

    • jamie says:
      10th December 2018 at 12:05 pm

      Email sent 🙂

      Reply

  • Dai says:
    4th August 2018 at 9:10 am

    Hi Jamie,

    Excellent work with these models – simply breathtaking. I’m a researcher at Aberystwyth University looking at diatoms to unravel past changes in climate. I’m also involved in a lot of outreach to local school and children to get them as excited about diatoms as I am! It would be great if you could share these files with myself so that I could use a few models along with my microscope slides to show off the beauty of the diatom world.

    Thanks,

    Dai

    Reply

    • jamie says:
      10th December 2018 at 12:05 pm

      Hi Dai, your work sounds very interesting. I’ve sent you an email with the files.

      Reply

  • Luis says:
    1st October 2018 at 5:00 pm

    Hello

    I was wondering if if you could send me the files so I can print my own model.

    Thanks.

    Reply

    • jamie says:
      10th December 2018 at 12:01 pm

      Hi Luis, just sent you an email with the files.

      Reply

  • Richard says:
    7th November 2018 at 8:38 pm

    Jamie,
    I work for the Maglab at Florida State University and somehow out geology department ran across your Diatom frustule on the ultimaker sight and inquired if I could SLA print them the model for educational purposes but I cannot seem to locate the STL files for it on the site, after a bit of digging I ended up here I was wondering if there was a way I could get a copy of the STL to print them a copy of your fantastic model?

    Thanks

    Reply

    • jamie says:
      10th December 2018 at 11:55 am

      Hello Richard,
      Thankyou for getting in touch.
      I’ve sent you and email with the files 🙂

      Reply

  • bryan ruiz says:
    4th December 2018 at 2:45 pm

    Dear Jamie,

    I am looking into the diatoms and I was wondering if you have the 3D model available to look at more closely?

    My main interest is in Campylodiscus Hibernicus Diatom.

    Would it be possible to get the model from you ? #

    Reply

    • jamie says:
      10th December 2018 at 11:53 am

      Email Sent 🙂

      Reply

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