Network motifs are small patterns of connections, found over‐represented in gene regulatory networks. An example is the negative feedback loop (e.g. factor A represses itself). This opposes its own state so that when ‘on’ it tends towards ‘off’ – and vice versa. Here, we argue that such self‐opposition, if considered dimensionlessly, is analogous to the liar paradox: ‘This statement is false’. When ‘true’ it implies ‘false’ – and vice versa. Such logical constructs have provided philosophical consternation for over 2000 years. (...) Extending the analogy, other network topologies give strikingly varying outputs over different dimensions. For example, the motif ‘A activates B and A. B inhibits A’ can give switches or oscillators with time only, or can lead to Turing‐type patterns with both space and time (spots, stripes or waves). It is argued here that the dimensionless form reduces to a variant of ‘The following statement is true. The preceding statement is false’. Thus, merely having a static topological description of a gene network can lead to a liar paradox. Network diagrams are only snapshots of dynamic biological processes and apparent paradoxes can reveal important biological mechanisms that are far from paradoxical when considered explicitly in time and space. (shrink)

We argue that the physics of complex materials and self-organizing processes should be made central to the biology of form. Rather than being encoded in genes, form emerges when cells and certain of their molecules mobilize physical forces, effects, and processes in a multicellular context. What is inherited from one generation to the next are not genetic programs for constructing organisms, but generative mechanisms of morphogenesis and pattern formation and the initial and boundary conditions for reproducing the specific traits of (...) a taxon. There is no inherent antagonism between this “physicalist” perspective and genetics, since physics acts on matter, and gene products are essential material components of living systems whose variability affects the systems’ parameters. We make this notion concrete by summarizing the concept of “dynamical patterning modules” (DPMs; Newman and Bhat, Phys Biol 5:1–14, 2008; Int J Dev Biol 53:693–705, 2009), an explicit physico-genetic framework for the origin and evolution of multicellular form in animals, as well as (when differences in interaction toolkit genes and applicable physical processes are taken into account) in multicellular plants (Hernández-Hernández et al., Int J Dev Biol 56:661–674, 2012). DPMs provide the missing link between development and evolution by revealing how genes acting in concert with physics can generate and transform morphology in a heritable fashion. (shrink)

In three recent articles it was shown that β‐catenin is crucial for the establishment and the maintenance of the overall polarity and especially for the character ‘posterior’ in planarians. If the transcription of the β‐catenin gene was silenced by RNA interference, the overall polarity is lost, and in regenerating fragments a posterior blastema displays anterior characters by forming eyes and anterior ganglia. An attempt is made to integrate these new data, well‐known older observations, and observations from other regenerating systems into (...) an outline of a model that will clarify our current understanding as well as highlight areas still to be developed. (shrink)

Biological mimicry is regarded by many as a textbook illustration of Darwin’s idea of evolution by random mutation followed by differential selection of reproductively fit specimens, resulting in gradual phenotypic change in a population. In this paper, I argue that some cases of so-called mimicry are probably merely look-a-likes and do not gain an advantage due to their similarity in appearance to something else. In cases where a similar appearance does provide a benefit, I argue that it is possible that (...) these forms of mimicry were created in a single generation. An interpretive response to an appearance as a sign can make a new structure perform drastically differently in an environment. In such cases, Darwin’s natural selection mechanism only helps to explain gradual the spread of these new forms, not the creation of them. I argue that biosemiosis should be regarded as a much more powerful mechanism for affecting evolutionary trajectories than the gradualist view allows. I focus on two cases of butterfly mimicry: the Viceroy (Nymphalidae: Limenitis archippus) and Monarch (Nymphalidae: Danaus plexippus) butterflies, supposed Müllerian mimics, and deadleaf mimic butterflies (Kallima). (shrink)

Proper wiring of the nervous system requires tight control of the number of nerve terminals that innervate a target tissue. Recent work by Deppmann et al.,1 now suggests that this is achieved by feedback‐mediated neuronal competition for target‐derived survival cues. The authors' model is inspired by the theory for pattern formation based on self‐activation and lateral inhibition, proposed by Meinhardt and Gierer more than 30 years ago.2 BioEssays 30:929–933, 2008. © 2008 Wiley Periodicals, Inc.

Peptides serve as important signalling molecules in development and differentiation in the simple metazoan Hydra. A systematic approach (The Hydra Peptide Project) has revealed that Hydra contains several hundreds of peptide signalling molecules, some of which are neuropeptides and others emanate from epithelial cells. These peptides control biological processes as diverse as muscle contraction, neuron differentiation, and the positional value gradient. Signal peptides cause changes in cell behaviour by controlling target genes such as matrix metalloproteases. The abundance of peptides in (...) Hydra raises the question of whether, in early metazoan evolution, cell–cell communication was based mainly on these small molecules rather than on the growth‐factor‐like cytokines that control differentiation and development in higher animals. BioEssays 23:420–427, 2001. © 2001 John Wiley & Sons, Inc. (shrink)