A weird chapter, 2nd of November 2012

For an unprepared reader, perhaps the weirdest part of my novel, >> Problem of the observer (Problem promatrača) is chapter XVIII, Octahedral time bomb. This is the chapter I needed to redirect the plot of the novel, although >> "Problem of the observer" is, of course, not a novel which importantly depends on its plot. The "plot" in "Problem of the observer" has the same role as peanuts do on a table with glasses of weissbier, surrounded by shiny, healthy and merry faces of people whose company we enjoy - it's good if there are peanuts, but if there aren't any, we'll have excellent fun nevertheless.

Before I sent the novel to the publisher, six or seven people read it, and two of them warned me about the chapter XVIII. One of them told me that it was not clear to him whether I tried to write a scientific paper or a chapter of a novel. Namely, in chapter XVIII, the company from Crick 14 discovers a virus in the Egghead's brain, but not just any virus, of course. It is a virus with octahedral symmetry, which means that it can be reduced to triangulation of the octahedron. The image below shows the triangulation process. In right-hand shape, each triangle might represent a single protein of a virus shell. The image above was published in a book and it shows how an "octahedral" virus might look like "for real", with all the protein "chunks" and "seams", and RNA molecule in its inside.

Of course, the viruses that we know are NOT triangulated octahedra. A large number of viruses can be represented as (sometimes chiral) triangulated ICOSAHEDRA. I have written about it several times on the pages of Construction of Reality, and those interested in it can read an introductory description I deposited in the ArXiv, >> Icosadeltahedral geometry of fullerenes, viruses and geodesic domes.

Early explorers of viruses considered the idea of viruses with different symmetries, which is not strange since they didn't have a detailed experimental insight we have today. So, famous Crick and Watson in the conclusion of their Nature paper from year 1956, say:

Crick and Watson also provide a table of possible virus symmetries where they also mention octahedral symmetry (below; from Crick & Watson, "Structure of small viruses", Nature 177 (1956)). Additional link between Francis Crick, viruses and "Problem of the observer" is the name of the research space station where the plot of the novel takes place - Crick 14.

The illustration for chapter XVIII, shown in the image which opened this post, in addition to the invented virus also shows its amino-acid content (the image below) and three-dimensional distribution of its atoms. This detailed description of the virus was made by brothers Jim and Joe Nguyen :) , and I extracted it from one of about a hundred deposited PDB virus files (the image below; the letters in the background of the 3D representation of the virus - in >> a paper we recently published, Anže Lošdorfer Božič analyzed all available PDB virus files in details).

Now when I explained octahedra, icosahedra, proteins and viruses a bit, perhaps the chapter will be somewhat more transparent... I reproduce it below in entirety, and you can also >> download it in PDF, together with the illustration of the octahedral virus.

XVIII. Octahedral time bomb

Despite the dream and lowered neuron activity, the network was still decaying. It became obvious that the reason for that cannot be only the neuronal overload. Something was eating up the network from inside, with a speed which was clearly and measurably increasing with time. Some malignant process found the place for its existence below the sensitivity threshold of the control mechanisms. Of course, calling something “a process” was avoiding giving a clear face to the cause, storing all that was unknown behind that word which does not suggest some separable material reality.

But the “process” had a completely material cause. Nguyens found it almost by accident because it was so small that it past unnoticed through most of the scanning protocols. The bastard’s appearance was beautiful, as it is for most members of his parasitic kin. Mathematically precise, most simple, but tiny and deadly. Forty eight proteins in total, arranged in clusters of three and four and positioned in a network with octahedral symmetry. It is possible that something like that was never discovered previously because its type of symmetry was irreconcilable with the icosahedral distribution of five- and six- protein clusters typical for huge majority of its explored cousins. This one was also fascinatingly small, only seven and a half nanometers in diameter. The amount of genetic information, and the twins were certain that it was the RNA molecule, which could be stored in such a limited space had to be less than anything previously known. Perhaps this was also the reason for a relatively slow propagation of the virus and dependence of its assembly on electrical processes in neurons. Perhaps it propagated only through the active, thinking matter. The thing which kills that which thinks. That would explain the slowing down of the neuronal damage in the state of lowered neural activity. “Tragic. Instead of the evolution of thinking processes, we evolved the virus which feeds on thoughts. A lovely end of the project.” Ehrenfest was sure that the virus was not formed by a mutation of some common virus brought in from the outside which would pollute the circulation of the Egg and pass through the blood-brain barrier. None of the activity protocols was ever broken. The geometrized bastard had to evolve from the inside. Perhaps catalyzed by the addressing of the inorganic matrix. This could explain its unusual symmetry. Nguyens thought that the virus was in the network for quite some time, and that its activity may have been additionally boosted by the usage of gamma-knife during the nubit separation. However it was, the thing was created from the pile of protein and RNA junk which was delayed somewhere, probably in the intercellular space, for long enough in order to be catalyzed by the electric field and inorganic substrate and assembled in a beautiful package with a ribbon. And a bomb inside.

A refined immune system was not a part of the Egghead’s architecture. There were no processes of immune memory and production of the antibody arsenal. Only basic modest machinery was developed, controlled completely from the outside, never before engaged, and totally inadequate for the situation. The twins isolated the virus culture and already performed some experiments on it but without any results. The virus mutated with a huge speed because it had no mechanisms to preserve its genetic making. Perhaps that was how it stumbled onto that weird octahedral symmetry and perhaps it was completely different only a couple of days ago. Its uncontrolled mutation would probably render it completely harmless for humans whose immune system would almost certainly deaden it already on the first day. It was difficult to say how dangerous it was in the present moment of its evolution, and Nguyens didn’t think about it at all.

According to the protocols prescribed by the Agency for such situations, the experiment should be immediately aborted, the laboratories hermetically sealed, all the conditions for the virus isolation should be ensured, the managing body on Earth should be contacted and the team of cleaners who would with utmost certainty disassemble all traced of the organic matter should be waited for. Nobody, of course, had any of this in mind, including the professor. He wanted another opportunity to speak to Egghead, but in the present situations, this did not seem probable. Although ever since he came to Crick everything progressed from bad to worse, he gained unusual trust in quiet and reliable twins, and he also did not consider Ernest’s state as psychosis anymore. It was a problem of consciousness. An untamed problem of conscience which may be bordering with psychosis, but which started from something professor could perfectly well understand. What he did not know is for how long Ernest knew that the border was crossed beyond which Egghead had to be considered … well, person. Perhaps even a human. Of course, in some sense deeper than “it has two legs and two arms”. How long was it since he recognized that the problem crossed the borders of scientific research and became the problem of conscience? Since when he knew that from a scientist seeking insight he became a doctor responsible for someone’s life? Since when he knew that “computer” and “model brain” are only untrue phrases which he used to hide himself from anxiety? The project’s experimental logs did not give the answer to this question, perhaps also because they were rearranged, but professor assumed that the situation lasted for at least several months. To create a crippled consciousness, the consciousness of a “machine”, “computer” or a prisoner? And to realize this fact in full only after this consciousness sinks behind the material substrate, escapes in a dream without an exit. That had to be painful. Claustrophobic. But Ernest accepted his nightmare. Even when he allowed the brain operation he knew that the responsibility was only his and that professor could not completely understand what he suggested, because he himself was also thinking about it for some time. He will take all the blame. The scorn of humanity and rage of bioethicists and religious fanatics who exiled him to the cold Crick 14. He will give meaning to their slogans which they could not give them.

He could, sorrowfully, give them a completely clear meaning.

Download >> chapter XVIII from "Problem of the observer" in PDF.

Last updated on 2nd of November 2012.