Rolie Barth replies to his critics: What have pufferfishes and plasmas in common?

pufferfish (Tetraodon mbu) (wikipedia)

In this blog I will give some more clarification about my previous blog Circular causality, another secret of life?, particularly to some remarks of Gert Korthof, which I repeat in my own words.

Gerts question is this: are all components of the systems (molecules, cells, regulatory networks) that self-organize into patterns or structures not gene products? ‘All physical processes you point out are not in 'a glass of water' or any artificial laboratory environment, no, always in a cell or an organism.’

Comparing the skin of a giant pufferfish (Tetraodon mbu) and the patterns of plasmas (a glow discharge) reveals that the skin pattern as well as other biological patterns are physical of nature. The resemblance demonstrates that mutations of genes and natural selection did not make the pattern, but selected it from physical possibilities.

First, let’s start with the pufferfish [1], what a beautiful skin pattern! (see picture above). Is this a unique biological phenomena? To answer this question we turn to plasma physics, a research field in which I have worked for more than 30 years  at the FOM Instituut voor Plasmafysica. My job was to measure the temperature of the plasma electrons. In most experiments particles in plasmas are not evenly distributed but many kind of patterns can appear.
Plasma physicists of the Working Group Purwins (University of Münster, Germany) have built devices to generate low temperature plasmas [2]. A plasma is an ionized gas with free moving ions and electrons which are able to conduct electrical current. Making such plasma between two parallel plates (electrodes) the physicists found all kind of patterns. The patterns show up at the two plates due to the plasma-surface interaction and are made visible using one transparent electrode. A digital camera is applied to record the images. The optical pattern corresponds to the current density pattern in the plasma.

At certain values of the AC voltage a pattern was found that is quite similar to that of a pufferfish. In the figure below tree patterns are shown: left – a pufferfish skin [1], middle – a pattern of the plasma surface interaction [2] and right – a simulation using the Gray-Scott model [3].
Comparing a part of the pufferfish skin (left) and a pattern of the plasma surface interaction show a remarkable resemblance. Indeed, they are not identical but a great similarity cannot be denied.

The third image (right panel) shows the result of simulations using some kind of Turing model, the so called Gray-Scott model. All these modeled processes belong to the large family of reaction diffusion processes for two ore more species of particles, which can be: electrons, ions, chemicals, morphogens, cells and also larger entities. Analyzing these reaction diffusion processes can partly be done analytical, but to determine patterns requires computer simulations.

So, what have pufferfishes and plasmas in common? In both cases reaction diffusion processes created similar patterns that correspond more or less to mathematical simulations of these phenomena. It is obvious that the patterns produced by the interaction of the plasma with the transparent plate (electrode) are the result of physical laws of nature without the need of any external information (like genes in the biological situation). This demonstrates that biological patterns like that of the pufferfish were not invented but discovered by evolutionary processes. These patterns result from physical mechanisms. Of course, in the biological pattern formation genes play important roles:
1. Most morphogens are proteins, build by genetic information.
2. Feedback loops of these systems consist of genetic networks and physical mechanisms, like diffusion.
3. Genes save information about how to reuse the physical process during next generations.
4. Contrary to purely physical processes, the biological variant of these processes can be modified by gene mutations or even by epigenetic processes.

Finally, the resemblance of pufferfish and plasma patterns also show some important features of the position information model of Lewis Wolpert, described by Marleen in reply to my previous blog. She wrote: “The patterning is well described, but can also be described by a simple gradient of morphogens that have to pass a threshold value”, where (in my own words) every threshold is genetically coded. This model is suitable to understand the creation of rather simple, linear patterns like the segments of insects, the swivels of backbones, tails of dino’s and the like. But simulating a pufferfish pattern with this model would require a lot more genetic information than describing it by a Turing model. The model of Wolpert requires two genetically coded threshold values for each stripe … In the Turing model the number of stripes and their separation distance is a matter of tuning two of the system parameters and not of adding new parameters.

In conclusion: the fact that the pufferfish skin pattern and plasma patterns show such close similarities clearly demonstrates that these patterns are generated by physical mechanisms. Of course, genes are not unimportant because they produce the morphogens and are part of the feedback loops necessary for the pattern generating processes. Under these patters lie the physical rules and mechanisms for the complex interaction of a large number of particles. Generally spoken, these patterns are formed by the collective behavior of interacting particles which are part of non-linear dynamical systems, like physical plasmas and biological tissue.

 

References

1. Pufferfish image: Wikipedia
2. Plasm pattern and plasma experimental setup: Juan Pablo Trelles, ‘Pattern formation and self-organization in plasmas interacting with surfaces’, 2016, J. Phys. D: Appl. Phys. 49, 393002, Figure 3. See also: H. -G. Purwins, 2011, IEEE Trans. Plasma Sci. 39-11, 2112.  
3. Simulated pattern: simulation for a Gray-Scott model, k = 0.61 and F = 0.42. Take look at this website with a extended simulator of such patterns: https://www.mrob.com/pub/comp/xmorphia/index.html.
    

hier nog een geweldige foto van de pufferfish !