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  • Print publication year: 2016
  • Online publication date: March 2016

10 - Walking the Tightrope: The Dilemma of Hierarchical Instabilities in Turing's Morphogenesis

from Part Three - The Reverse Engineering Road to Computing Life

Summary

Dedicated to Bashir Ahmad and a bright future for physics in his Afghanistan.

Ever since we understood that living organisms are made of fundamentally the same stuff as the rest of the universe, we have been puzzling about what makes life different, and how that difference arose. Alan Turing made a major contribution in putting forth a model for morphogenesis that attempts to bridge the gap between the molecules we are made of and how we look. This is a huge gap to span in trying to solve the problem of how an embryo builds itself. People are about 1.5m = 1.5×109nm (nanometers) tall and the typical protein molecule is about 30 nm wide, a ratio of 50 000 000 = 5 × 107 to 1. That protein might contain 1000 amino acids and, if we take into account the relative volumes, not just length, say 70 liters for an adult human and 0.15nm3 for an amino acid (Sühnel and Hühne, 2005), this raises the ratio to 5×1026 to 1.

When we build a bridge, unless it's over a small ditch, we use many parts and assemble them in sections called spans (Figure 10.1). In biology this has come to be known as ‘modularity’, and the grand search has been on to discover just what the modules of life are (von Dassow and Munro, 1999; Gilbert and Bolker, 2001; Redies and Puelles, 2001; Newman and Bhat, 2009; Peter and Davidson, 2009; Christensen et al., 2010). At first it was thought that cells represented modules. The ‘cell theory’ was resisted by a minority of 19th century biologists, who thought that the basic module was the whole organism, not the cell. Certain observations support this ‘organismal’ theory. First, single cell organisms, such as Parameciumand diatoms (Figure 10.2), can have quite complex morphologies; see Gordon (2010); Tiffany et al. (2010); Gordon and Tiffany (2011). Second, some green algae have many nuclei that move in cytoplasmic streaming, unhindered by cell boundaries, yet “… exhibit morphological differentiation into structures that resemble the roots, stems, and leaves of land plants and even have similar functions” (Chisholm et al., 1996); see Cocquyt et al., 2010.

Alicea, B., McGrew, S., Gordon, R., Larson, S., Warrington, T. and Watts, M. (2014). DevoWorm: differentiation waves and computation in C. elegans embryogenesis. Available at http://www.biorxiv.org/content/early/2014/10/03/00999 [Accessed March 26, 2015].
Bard, J.B.L., Baldock, R.A. and Davidson, D.R. (1998a). Elucidating the genetic networks of development: a bioinformatics approach.Genome Res., 8 (9), 859–63.
Bard, J.B.L., Kaufman, M.H., Dubreuil, C., Brune, R.M., Burger, A., Baldock, R.A. and Davidson, D.R. (1998b). An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech. Dev., 74 (1/2), 111–20.
Beloussov, L.V. and Gordon, R. (2006). Preface. Morphodynamics: Bridging the gap between the genome and embryo physics. Int. J. Dev. Biol., 50 (2/3), 79–80.
Björklund, N.K. and Gordon, R. (1994). Surface contraction and expansion waves correlated with differentiation in axolotl embryos. I. Prolegomenon and differentiation during the plunge through the blastopore, as shown by the fate map. Computers & Chemistry, 18 (3), 333–45.
Blanchard, P. and Hongler, M.-O. (2002). How many blocks can children pile up? Some analytical results. J. Phys. Soc. Japan, 71 (1), 9–11.
Brodland, G.W., Gordon, R., Scott, M.J., Björklund, N.K., Luchka, K.B., Martin, C.C., Matuga, C., Globus, M., Vethamany-Globus, S. and Shu, D. (1994). Furrowing surface contraction wave coincident with primary neural induction in amphibian embryos. J. Morphol., 219 (2), 131–42.
Bulić-Jakuš, F., Ulamec, M., Vlahović, M., Sinčić, N., Katušić, A., Jurić-Lekić, G., Šerman, L., Krušlin, B. and Belicza, M. (2006). Of mice and men: teratomas and teratocarcinomas. Collegium Antropologicum, 30 (4), 921–4.
Chisholm, J.R.M., Dauga, C., Ageron, E., Grimont, P.A.D. and Jaubert, J.M. (1996). ‘Roots’ in mixotrophic algae. Nature, 381 (6581); erratum, 382 (6583) 565.
Christensen, D.J., Campbell, J. and Stoy, K. (2010). Anatomy-based organization of morphology and control in self-reconfigurable modular robots. Neural Comput. Appl., 19 (6), 787–805.
Cobb, M. (2006). Generation: The Seventeenth-Century Scientists Who Unraveled the Secrets of Sex, Life, and Growth. Bloomsbury.
Cocquyt, E., Verbruggen, H., Leliaert, F. and De Clerck, O. (2010). Evolution and cytological diversification of the green seaweeds (Ulvophyceae). Mol. Biol. Evol., 27 (9), 2052–61.
Crampin, E.J., Gaffney, E.A. and Maini, P.K. (1999). Reaction and diffusion on growing domains: scenarios for robust pattern formation. Bull. Math. Biol., 61 (6), 1093–120.
Damer, B., Newman, P., Norkus, R., Gordon, R. and Barbalet, T. (2012). Cyberbiogenesis and the EvoGrid: a twenty-first century grand challenge. In Genesis – In the Beginning: Precursors of Life, Chemical Models and Early Biological Evolution.J., Seckbach (ed.). Springer, pp. 267–88.
Dennett, D.C. (1995). Darwin's Dangerous Idea: Evolution and the Meanings of Life. Simon & Schuster.
Evsikov, S.V., Morozova, L.M. and Solomko, A.P. (1994). Role of ooplasmic segregation in mammalian development. Roux's Arch. Dev. Biol., 203, 199–204.
Fankhauser, G. (1941). Cell size, organ and body size in triploid newts(Triturus viridescens). J. Morphol., 68, 161–77.
Fankhauser, G., Vernon, J.A., Frank, W.H. and Slack, W.V. (1955). Effect of size and number of brain cells on learning in larvae of the salamander, Triturus viridescens. Science, 122 (3172), 692–3.
Fleury, V. and Gordon, R. (2012). Coupling of growth, differentiation and morphogenesis: an integrated approach to design in embryogenesis. In Origin(s) of Design in Nature: A Fresh, Interdisciplinary Look at How Design Emerges in Complex Systems, Especially Life.L., Swan, R., Gordon and J., Seckbach (eds.). Springer, pp. 385–428.
Gilbert, S.F. and Bolker, J.A. (2001). Homologies of process and modular elements of embryonic construction. J. Exp. Zool., 291 (1), 1–12.
Gilbert, S.F. and Epel, D. (2009). Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution. Sinauer Associates.
Gordon, N.K. and Gordon, R. (2015). Embryogenesis Explained. World Scientific.
Gordon, R. (1966). On stochastic growth and form. Proc. Natl. Acad. Sci. USA, 56 (5), 1497–504.
Gordon, R. (1999). The Hierarchical Genome and Differentiation Waves: Novel Unification of Development, Genetics and Evolution. World Scientific and Imperial College Press.
Gordon, R. (2006). Mechanics in embryogenesis and embryonics: prime mover or epiphenomenon?Int. J. Dev. Biol., 50 (2/3), 245–53.
Gordon, R. (2008). Hoyle's tornado origin of artificial life, a computer programming challenge. In Divine Action and Natural Selection: Science, Faith and Evolution, J., Seckbach and R., Gordon (eds.). World Scientific, pp. 354–67.
Gordon, R. (2009). Google Embryo for building quantitative understanding of an embryo as it builds itself: II. Progress toward an embryo surface microscope. Biological Theory: Integrating Development, Evolution, and Cognition, 4 (4), 396–412.
Gordon, R. (2010). Diatoms and nanotechnology: early history and imagined future as seen through patents. In The Diatoms: Applications for the Environmental and Earth Sciences,J.P., Smol and E.F., Stoermer (eds.). Cambridge University Press, pp. 585–602.
Gordon, R. (2011). Epilogue: the diseased breast lobe in the context of x-chromosome inactivation and differentiation waves. In breast cancer: a lobar disease,T., Tot (ed.). springer, pp. 205–10.
Gordon, R., Björklund, N.K. and Nieuwkoop, P.D. (1994). Dialogue on embryonic induction and differentiation waves. Int. Rev. Cytology, 150, 373–420.
Gordon, R. and Brodland, G.W. (1987). The cytoskeletal mechanics of brain morphogenesis. Cell state splitters cause primary neural induction. Cell Biophysics, 11, 177–238.
Gordon, R. and Hoover, R.B. (2007). Could there have been a single origin of life in a Big Bang universe? Proc. SPIE, 6694, doi:10.1117/12.737041.
Gordon, R. and Melvin, C.A. (2003). Reverse engineering the embryo: a graduate course in developmental biology for engineering students at the University of Manitoba, Canada.Int. J. Dev. Biol., 47 (2/3), 183–7.
Gordon, R. and Tiffany, M.A. (2011). Possible buckling phenomena in diatom morphogenesis. In The Diatom World, J., Seckbach and J.P., Kociolek (eds.)., Springer, pp. 245–72.
Gordon, R. and Westfall, J.E. (2009). Google Embryo for building quantitative understanding of an embryo as it builds itself: I. Lessons from Ganymede and Google Earth.Biological Theory: Integrating Development, Evolution, and Cognition, 4 (4), 390–5, with supplementary appendix.
Graham, J.H., Freeman, D.C. and Emlen, J.M. (1993). Antisymmetry, directional asymmetry, and dynamic morphogenesis.Genetica, 89 (1/3), 121–37.
Hellige, J.B. (1993). Hemispheric Asymmetry, What's Right and What's Left.Harvard University Press.
Hermeyer, D. and Wantman, S. (2008). Kingston–Rhinecliff bridge. Available at http://en.wikipedia.org/wiki/File:Kingston-Rhinecliff_Bridge2.JPG [Accessed July 13, 2011].
Howard, J., Grill, S.W. and Bois, J.S. (2011). Turing's next steps: the mechanochemical basis of morphogenesis.Nature Rev. Molec. Cell Biol., 12 (6), 392–8.
Hwang, S.Y. and Rose, L.S. (2010). Control of asymmetric cell division in early C. elegans embryogenesis: teaming-up translational repression and protein degradation.BMB Rep., 43, (2), 69–78.
Ishihara, S. and Kaneko, K. 2006. Turing pattern with proportion preservation.J. Theor. Biol., 238 (3), 683–93.
Iwasaki, S. and Honda, K. (2000). How many blocks can children pile up? – Scaling and universality for a simple play.J. Phys. Soc. Japan, 69, (6), 1579–81.
Jaffe, L.F. (1999). Organization of early development by calcium patterns.BioEssays, 21 (8), 657–67.
Lopez, D., Vlamakis, H. and Kolter, R. (2009). Generation of multiple cell types in Bacillus subtilis.FEMS Microbiol. Rev., 33 (1), 152–63.
Maini, P.K., Woolley, T., Gaffney, E. and Baker, R. (2015). Turing's theory of developmental pattern formation. In The Once and Future Turing – Computing the World.S., Barry Cooper and A., Hodges (eds). Cambridge University Press, pp. 137–49.
Maurer, U. (2015). Cryptography and computation after Turing. In The Once and Future Turing – Computing the World.S., Barry Cooper and A., Hodges (eds). Cambridge University Press, pp. 54–78.
Meeks, J.C., Campbell, E.L., Summers, M.L. and Wong, F.C. (2002). Cellular differentiation in the cyanobacterium Nostoc punctiforme.Arch Microbiol., 178 (6), 395–403.
Newman, S.A. and Bhat, R. (2009). Dynamical patterning modules: a ‘pattern language’ for development and evolution of multicellular form.Int. J. Dev. Biol., 53 (5/6), 693–705.
Nikas, Y. (2011). Human egg in the fallopian tube [#470]. Available at http://www. eikonika.net/v2/photo_info.php?photo_id=470 [Accessed July 25, 2011].
Parisi, J. (1991). Global symmetry aspects of a compartmentalized reaction–diffusion system.Comp. and Math. Appl., 22 (12), 23–31.
Peter, I.S. and Davidson, E.H. (2009). Modularity and design principles in the sea urchin embryo gene regulatory network.FEBS Lett., 583 (24), 3948–58.
Rayleigh, Lord (1892). On the instability of a cylinder of viscous liquid under capillary force.Phil. Mag., 34, 145–54.
Redies, C. and Puelles, L. (2001). Modularity in vertebrate brain development and evolution.BioEssays, 23 (12), 1100–11.
Reid, R.G.B. (1985). Evolutionary Theory: The Unfinished Synthesis.Croom Helm.
Rosen, R. (1968). Turing's morphogens, two-factor systems and active transport.Bull. Math. Biophys., 30 (3), 493–499.
Sharov, A.A. and Gordon, R. (2013). Life before Earth. Available: http://arxiv.org/ abs/1304.3381.
Sühnel, J. and Hühne, R. (2005). The Amino Acid Repository. Available at http://www. imb-jena.de/IMAGE_AA.html [Accessed July 13, 2011].
Tiffany, M.A., Gordon, R. and Gebeshuber, I.C. (2010). Hyalodiscopsis plana, a sublittoral centric marine diatom, and its potential for nanotechnology as a natural zipper-like nanoclasp.Polish Botanical J., 55 (1), 27–41.
Tokumitsu, N. and Honda, K. (2005). Crossover scaling in piling block games.J. Phys. Soc. Japan, 74 (6), 1873–4.
Tomanek, B., Hoult, D.I., Chen, X. and Gordon, R. (2000). A probe with chest shielding for improved breast MR imaging.Mag. Res. Med., 43 (6), 917–20.
Turing, A.M. (1952). The chemical basis of morphogenesis.Phil. Trans. Roy. Soc. London, B237, 37–72.
Tuszynski, J.A. and Gordon, R. (2012). A mean field Ising model for cortical rotation in amphibian one-cell stage embryos.BioSystems, 109 (3), 381–9.
von Dassow, G. and Munro, E. (1999). Modularity in animal development and evolution: elements of a conceptual framework for EvoDevo.J. Exp. Zool., 285 (4), 307–25.
Watson, R.A. (2006). Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution.MIT Press.
West-Eberhard, M.J. (2002). Developmental Plasticity and Evolution.Oxford University Press.
Zernicka-Goetz, M. (2011). Proclaiming fate in the early mouse embryo.Nat. Cell Biol., 13 (2), 112–14.