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	Figure 1. Interplay of genetics and physics. (A) The process of developing an organism from a fertilized egg cell involves an interplay of physics and genetics. Transcriptional gene-regulatory networks (GRNs) specify the production of effector proteins that allow coupling to specific physical processes (adhesion, tension, electric propagation, diffusion, etc.). It is the emergent order in those physical processes that ultimately results in a specific 3-dimensional shape of the body and its internal organs. (B) At least 3 codes participate in this process. The genetic code, which maps DNA sequence to protein sequence, controls cell behavior. The Epigenetic code, which maps chromatin state to expression of specific genes, regulates cell type and physiological properties. The bioelectric code maps the distribution of endogenous voltage gradients and electric fields in vivo, and appears to regulate large-scale anatomical patterning.54,55,75,108
	Figure 2. Bioelectric networks and their modulation. Many tissues, not only the nervous system, maintain active electrical communication among cells. Developmental bioelectricity, as in neurons, relies on ion channels and pumps to produce resting potential gradients across their cell membranes, and gap junctional channels to spread those potentials to neighboring cells. Signals within this network are mediated by the transfer of current and small molecules such as neurotransmitters. Because many ion channels and gap junctions are themselves voltage-sensitive, this system can support complex dynamics; the output of these dynamics includes changes in gene expression and cell behavior, mediated by transduction machinery such as neurotransmitter flux. Experimental (and endogenous) modulation of these dynamics can occur via regulation of gap junctional connectivity within the network (targeting gap junctions to alter plasticity of the electrical synapses), changes in ion channel activity (editing of resting potentials as a kind of intrinsic plasticity), or direct effects on the resulting gradients of neurotransmitters. A wide variety of genetic, pharmacological, and optical tools are now available to manipulate physiological networks in developmental or regenerative contexts in vivo. Graphics by Alexis Pietak.
	Figure 3. Changes to species-specific head shape in planaria. Physiological determination of species-specific head anatomy in the planarian flatworm. Transient exposure to octanol after amputation in G. dorotocephala results in regeneration of head anatomies resembling other species of planarian. Brain shape and distribution of neoblasts is also altered. Shape change can be quantified using geometric morphometrics, and used to produce a shape space accounting for much of the variation in shape between species. (A) Wild type G. dorotocephala morphology. (Ai) pseudo G. dorotocephala morphotype after octanol treatment. (Aii) brain morphology of pseudo G. dorocephala morphology by anti-synapsin immunostaining. (Aiii) neoblast distribution of pseudo G. dorotocephala morphology by anti-phosphorylated histone 3 immunostaining. (Aiv) wild type G. dorotocephala brain morphology and neoblast distribution. (B) Wild type D. japonica morphology. (Bi) pseudo D. japonica morphotype after octanol treatment. (Bii) brain morphology of pseudo D. japonica morphology by anti-synapsin immunostaining. (Biii) neoblast distribution of pseudo D. japonica morphology by anti-phosphorylated histone 3 immunostaining. (Biv) wild type D. japonica brain morphology and neoblast distribution. (C) Wild type S. mediterranea morphology. (Ci) pseudo S. mediterranea morphotype after octanol treatment. (Cii) brain morphology of pseudo S. mediterranea morphology by anti-synapsin immunostaining. (Ciii) neoblast distribution of pseudo S. mediterranea morphology by anti-phosphorylated histone 3 immunostaining. (Civ) wild type S. mediterranea brain morphology and neoblast distribution. (D) wild type P. felina morphology. (Di) pseudo P. felina morphotype after octanol treatment. (E) CVA analysis of wild type morphologies and pseudo morphologies, with morphometric landmarks shown on a wild type G. dorotocephala head. Figures used with permission from ref. 163.
	Figure 4. Morphogenetic state spaces. A conceptual model of shape change driven by physiological network dynamics. Planaria regeneration parallels classical neural network behavior; both can be described in terms of free energy landscapes with multiple attractor states. (A) Behavior of a classical Hopfield neural network trained to reproduce 3 types of patterns, in this case shapes of the letters ‘F’, ‘H’, or ‘G’, which are the 3 stable states of the network's free energy landscape. The state of the Hopfield network's nodes directly relate to the brightness of pixels on a display, generating output. Perturbation of the network from a stable state (red arrow) by deleting (damaging) part of the pattern is akin to moving a ball to an unstable point on the free energy landscape, and leads to regeneration of the closest learned attractor state (blue arrow). In this, such networks' well-known ability to implement memory is analogous to regenerating organisms restoring a specific target morphology upon damage. (B) The parallel concept of planaria regeneration into head shapes of one of 3 different species, which are attractor states of the free energy landscape. Outcome morphology is driven by the dynamic outputs of physiological cellular network. Amputation (red arrow) is akin to moving the system to an unstable point on the free energy landscape. Normal regeneration would return the system to its main attractor, but altering cell network dynamics via gap junction blockade allows for regenerative transitions (blue arrow) to alternative local minima, corresponding to morphospace regions normally occupied by P. felina and S. mediterranea worms. In time, remodeling (green arrow) transfers these morphologies to the global minimum of the wild-type state (G. dorotocephala). (C) Morphospaces are conceptual structures within which distances along specific metrics can represent the differences among species' morphologies. This panel illustrates how variants in the shape of a structure (skull shapes in this case) can be represented in a virtual space describing several orthogonal control parameters. We suggest that the physiologically-induced conversion of an animal with a normal genome into a different species-specific morphology could be modeled by an appropriate bioelectric circuit model whose measured states control relevant parameters forming the axes of a morphospace. Such spaces often include stable attractors corresponding to anatomical configurations that stable to small perturbations of the key parameters. (D) It is possible that the global coordinate axes that facilitate the Thompson transformations are mediated by bioelectric field properties across the organism. Images used with permission as follows: A,B,163 C,113 D.115
	Figure 5. Unexplored regions of morphospace reached by editing bioelectric circuits. Briefly altering bioelectric circuit dynamics, despite the presence of a normal genome, can result in drastic alterations of the bodyplan, to regions not currently occupied by extant species. D. japonica worms treated with disruptors of gap junctional connectivity or modulators of ion channel-depenedent bioelectric signaling can acquire compound (A), spiky (B), or cup-shaped (C) morphologies instead of the genome-default flat architecture of the planarian. The specimen in panel D has been stained with an antibody to reveal the central nervous system, and cleared to highlight the pocket-like morphology. In some cases, these edits to the normal target morphology can be permanent (E): a flatworm middle fragment that regenerates 2 heads after a brief reduction of bioelectrical coupling among its cells will continue to regenerate as 2-headed in subsequent cuts made in plain water. Even if the “reprogrammed” head tissue is removed, the target morphology information in other fragments of the body have been physiologically altered so that a 2-headed form results. This new worm architecture has distinct behavioral and anatomical structures and is stable across the most common mode of reproduction in this species (fission + regeneration), stretching the definition of speciation. (F) Changes of head shape (red arrowhead) and number (yellow arrow) can occur in the same animal, as can changes in head size (G, red arrow). Editing of large-scale bodyplan can be induced in vertebrate models as well, inducing ectopic eye growth out of gut tissue (red arrow), and ectopic limb growth out of the mouth (I, red arrow). Images used with permission as follows: E,53 G,124 H.67 Photo in panel I courtesy of Erin Switzer.
	Figure 6. Altering neurotransmitter signaling induces inter-species shape changes in Xenopus tadpoles. (A) Treatment with the β-adrenergic agonist Cimaterol (CIM) stochastically induced 4 distinct head anatomies. Embryos were exposed to CIM from st. 10-45, sacrificed at st. 47 and stained with Alcian blue. (i) Wild-type Xenopus tadpole with major ventral craniofacial cartilages labeled on one side of the face. Meckel's cartilage (m) is outlined in Pink, ceratohyal cartilage (c) is outlined in green, and the branchial arches (ba) are outlined with yellow. (ii) Tadpole with malformed jaw, but otherwise normal craniofacial morphology. (iii) Tadpole with horizontal or “flat” branchial arches and ceratohyal cartiages. (iv) Tadpole whose head anatomy visually resembles that of Rana frogs. (v) Tadpole whose head anatomy resembles that of frogs belonging to the family Microhylidae. (B) Comparison of Pseudo Rana head morphology to that of wild-type Rana species. (i) Graphical output for Canonical Variate analysis of shape data in wild-type and experimentally-derived craniofacial morphologies, showing confidence ellipses for means at an 0.9 probability. Each point represents one individual's face shape data. Data for wild-type Rana frogs were derived from anatomical diagrams of Rana temporaria,130 Rana dalmatina,132 and Rana palustris.131 (ii) ventral view of alcian-blue stained Pseudo rana tadpole with landmarks (black dots) used for morphometric analysis. (iii) Anatomical diagram of ventral craniofacial skeleton of Rana temporaria tadpole. For both ii and iii, protruding nasal cartilages are indicated with red arrows, Meckel's cartilages are outlined in pink, and branchial arches are outlined in yellow. (C) Comparison of Pseudo Microhylidae head morphology to that of wild-type Microhylidae species. (i) Graphical output for Canonical Variate analysis of shape data in wild-type and experimentally-derived craniofacial morphologies, showing confidence ellipses for means at an 0.9 probability. Each point represents one individual's face shape data. Data for wild-type Microhylidae frogs were derived from anatomical diagrams of Microhyla ornata,133 Gastrophryne carolinensis,134 and Dermatonotus muelleri.135 (ii) ventral view of alcian-blue stained Pseudo Microhylidae tadpole with landmarks (black dots) used for morphometric analysis. (iii) Anatomical diagram of ventral craniofacial skeleton of a Microhyla ornata tadpole. For both ii and iii, ceratohyal cartilages are outlined in green, and branchial arches are outlined in yellow.

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