Chaos

And we lived beneath the waves.
And above us she arose from the sea foam
Aphros! We shouted
From the confines of our yellow submarine
we watched death of the father of the gods
And above us she arose from the sea foam
Aphros! We shouted
while we all lived in a yellow submarine.
  .’ said Jano.

‘Do I know you?’’ asked harry

‘Yes, you do. I took you to the cinema to see Elvis and then they shot me few months after that. You were only 12 and your mother asked me to protect you so I did.’ Answered Jano.

‘Hmm’. Answered harry. ‘What do you know about chaos and strange attractors, Jano?’

‘Let me consult the Chicago élite headed by boeing 777 and I cite: Chaos theory is a branch of mathematics that deals with nonlinear dynamical systems. A system is simply a set of interacting components that form a larger whole. Nonlinear means that due to feedback or multiplicative effects between the components, the whole becomes something greater than the mere sum of its individual parts. Dynamical means changing as opposed to static. Chaos fundamentally indicates that there are limits to knowledge and prediction because some futures may be unknowable with any precision. Further, interventions into a system may have unpredictable outcomes even if the intervention is very minor, as tiny effects can compound (butterfly effect) or be damped nonlinearly over time.’

‘Chaos is an unformed mass, where all the elements are jumbled up together in a “shapeless heap’ chipped in Ovid. ‘’

‘Ordo ab chao – out of chaos, comes order’ chipped in the mind.

Chaos is when the present determines the future, but the approximate present does not approximately determine the future” said Lorenzo

‘Huh’ said harry. ‘Slow down, Jano and Ovid, Lorenzo and you – the mind! You all say that a system of interacting components in chaos or so called chaotic system (do not say RANDOM!) overtime settles into spontaneous order, which is dependent on initial conditions of the system. And that we cannot break down the system into parts and understand its dynamics.

The mind citing boeing 777 again:

‘Spontaneous order or Strange attractors are globally stable, 
yet locally unstable: they have basins of attraction, yet within
 a strange attractor, infinitesimally close points diverge over time 
without ever leaving the attractor’s confines.’

‘You mean that LD (linkage disequlibrium) units, once formed following some initial conditions, are stable but can diverge overtime? But can we really refer to this divergence as genetic drift? And one would expect genetic sweeps after formation of a fabulously advantageous to life strange attractor ‘said harry.

‘Yip, yipee’ said Ovid. ‘Have you red my magnum opus Metamorphoses, harry? Do you agree that body is mortal and soul is immortal, harry? Ovid asked harry.’

‘I prefer Hesiod’s Theogony. Your source! And I believe a body is tied up to its own mind. When body dies mind dies as well (unless one cuts the head off and puts it on a spike and feeds it sugar; the whole process also needs energy in order to keep the head in sterile conditions).’ Answered harry. ‘What do you think about it all, Charles I?’

‘There is also a deep link between chaos and fractals. Fractals are shapes that are self-similar, meaning they have the same structure at every scale. Visualise leaf of a fern, which consists of the self-similar repeating units, which look the same at whatever level you are zooming in’ Said the mind.

‘Not so in real life’ said harry. ‘Consequence of asexual reproduction, I guess’.

‘Let me go back to the basins of attraction’ said harry.

Ok, said the mind. Let me searchenginase for you. The framed wolf says that

'basins of attraction are SET OF POINTS in the space of system variables 
such that initial conditions chosen in this set dynamically evolve to a 
particular attractor'.

‘Meaning that LD will be of a certain size (hence we have genes in core LD (attractor) and genes in wider LD (basins of attraction)’. Added harry. ‘And some people estimated that it was about 10cM.

‘Let me continue!’ said rather irritated mind. ‘The framed wolf also says and I cite:

'An attractor is a set of states (points in the phase space), invariant 
under the dynamics, towards which neighboring states in a given basin of
 attraction asymptotically approach in the course of dynamic evolution'.

‘Meaning that attractor (core LD) will be immutable and basins of attraction (or wider LD), described poetically as curves that never touch the attractor, can be happily recombined and combined again following the system perturbations such as inter-systemic fusion (inter-specific hybridisation?). In the normal species specific reproduction perturbation to the system would be minimal.’ said harry.

‘Let me finish!’. The mind is becoming rather impatient while citing the framed wolf again.

‘An attractor is defined as the smallest unit which cannot be itself 
decomposed into two or more attractors with distinct basins of attraction.
This restriction is necessary since a dynamical system may have multiple
attractors, each with its own basin of attraction.’

‘So I am right’! harry is basking in the sunlight of his ingenuity. ‘There are numerous core LDs with their own wide LDs in the genomes of every living thing on this planet!. Some are early eukaryote specific, some mammal specific – but essentially all formed under the same underlying principle!!

‘What happened to all those fellowships you applied for since 2011.’ Asked Ovid.

‘Nothing. ‘said harry. ’They were too stupid to understand my proposal and I was supposed to die of brain cancer since the Impervirous College London in 2011 under the royal baton (see chapter 29) infected me with it. The quasi super-intelligent projectiles that run NERcon said they did not support projects on crops (!) and trigger friendly squires of BBsrCommune said I did not deserve any money because I was unemployed.

‘Huh, up the river Hron with them! ‘said ovid. ‘You forgot to mention the Northern witch ceres (goddess of the crops), who preferred physics graduate with her regurgitated ideas of predator-prey models, which were supposed to approximate the dynamics of disease (predator) versus crop yield (prey). Too many approximations, I say, and no precision. ‘concluded ovid.

‘Could we solve the conundrum of cancer with your ideas, harry?’ asked Lorenzo. ‘Pity that you were not sent to Moscow University to study with Kolmogorov. Imagine that!. ‘Lorenzo is musing over the spilt milk.

‘Yeah, Harry is laughing’. ‘Math teacher hated me and taught me a first lesson in statistics and errors, which can lead to butterfly effect. You know – rounding up numbers to the closest integer in calculations. She rounded up my mark to 2 instead of 1 and told me, that I was just outside of the confidence interval for 1. And to compound her hate towards me she gave the same mark to the stupidest girl in the class – Ida (aka bowine fever). This kuwik located in the girl’s brain was apparently just inside the confidence interval for 2. During the oral exam I pulled out 2 questions (1). Basics of euclid geometry (2) solve difficult differential equation. Let’s say I got 2 for the question 1 (I forgot all the axiomatic definitions, which we were supposed to memorise) and 1 for the solving differential equation. The oral examiner, who was rather impressed with answer 2 did not want to rounded the mark to 2, but she persuaded him to do so.’ Concluded harry

‘All because harry was supposed to breed asap and not become a scientist. It would be rather difficult to do the breeding under the watchful eye of the King of the Boyars, who took shine to the little child, who survived on her own aboard the first orbital station for 80 days from 19.4.71- 7.6.1971 and also survived the landing. So rounding up the mark to 2 was actually deliberate effort on the part of the match teacher (controlled by bowine fever). King of the boyars did not give up (until he died) and sent his cleverest plant scientists down to influence her.

I think it worked.’ Said Charles the first. ‘BTW, harry, I also hate those gargantuanly granted backsides belonging to quasi bombshells at camvaults who were controlled by old revolting men, like bowine fever, and who bullied you so much just because they thought you were queen of the night, S. Quarto and many others. I completely agree with you expressing your anger in the way you did and do!. Well done!. There is nothing worth than bottling up ones anger or frustrations like I did during my lifetime. They put my head on spike in order to punish and belittle me and I was made into a saint. And my not bloodline descendants now want to have their head on spike as well and live for eternity. ‘Charles I started laughing.

‘Many others?’ asked Jano. ‘I only knew of jokoone and abbie’s Agnieska S. She did not tell me about quarto.’

‘Stop all these pointless rumblings about who is controlling whom!’ said Charles I. ‘Microservices are being developed to run certain discrete units, such as reproduction or house cleaning etc., so soon there will be no need for controllers. Everybody will be automated and run a software suit necessary for his/her/it existence and hopefully have ability to wake up and realise its surrounding if  new or unexpected appears and subsequently adapt (as animals do!). There will a lot of ‘outdated’ human software for resale. This modular system (microservices) will probably mean that software, once created, will last longer but never as long as an intelligent human, who can combine core modules, and thus adapt adaptively and efficiently without compromising storage capacity of his/her brain. I think biological organism are more than a suit of modular software units. A whole is more than a sum of its components parts! Intel people said that for neural network software subjects based on Harry’s mind patterns the controllers are using Pavlovian (pain causing buttons) if the software subject is not following instructions!. I want to know how you harry would solve cancer conundrum with your ideas’ asked Charles I harry. ‘You applied twice for a fellowship at that institute run by cyborgs for cyborgs. What happened? They were unable to put 2 and 3 together and come to a conclusion that pure DNA can only mean pure mind. ‘asked Charles I

‘2 and 3 together?’ harry started giggling. ‘Will you campaign for a gun-powder prize for me if I do?’ I am so lonely, have no money, nobody to talk to, nothing nice to look forward to and you want me to help those, who tried to kill me. How very easy-jeezy of you! ‘said harry and starting ranting and not wanting to air his fears about precision software for remote spies using touch. Perfection is your own enemy in this case. 

Hej jeezzz, co dá ti pláč,
Всю жизнь нести проблем не надо ношу.
Svět je krásnej, svět je zlej,
hej jeezzz, věř v něj,
Hej Jeez, že má tě ráda,
to se v písních tak snadno zpívá.
A do těch ran ti sype sůl a láme hůl. Oči pálí a slzy zebou.
to se v písních tak snadno zpívá.
 Запомни, нужно сердце приоткрыть,
 Чтоб сделать жизнь немного лучше.

Na rubu všech písní, kde končí rým,
tam prý leží stín, který nám zbývá.

Tak jen pojď sem, já půjdu tam,
hej jeezzz, já te ráda mám.

‘That is an interesting interpretation’ said Jano. ‘But, for well you know that it’s a fool who plays it cool.’

‘You are such a grandad, Jano’ said ovid. ‘Is that ’cool’ coming from oxford dictionary or from the urban one?’

‘Harry pleaseee’ interjected Charles I. ‘Cancer conundrum!’

‘Too complicated to sum it up with one sentence. Read my latest work at university, which gave S. quarto honorary doctorate in music. The super cool person full of hate because he had to lent his body to somebody else in order to advise me on how to stagger- iterate in loops rounded my mark as well. How very kind of him!‘ said harry. ‘He also said that my code was not in tune with my intro and that my code was not original, because I merely converted work written in C++ into java8. I must admit I was flattered when he rounded me down for being C++ expert. It tickled my pride. This must be a quantum world we live in, where rounding up is as bad as rounding down.’ Said harry rather perplexed.

‘Hey harry’ said Lorenzo. ‘Round up or down – i.e. to the closest integer always leads to errors – no matter how many cell you engage in order to achieve perfect precision. Can’t you see that?

‘Well, that is the very big problem of bioinformatics and the whole process of bioilluminati parallel -seq platforms in combo with ‘do not throw away anything away’ antiquated algorithms. How can you aim at and destroy the enemy, which is approximately here, there and maybe everywhere? This ‘enemy’ and one could also say ‘everybody is their own worst enemy’ is able to use your energy and water supply in order to consume you from the inside so that the other ‘you’ is reborn again. Get it – this enemy is you, yourself. It is your own individual cells revolting against the clonal body (you). And at the same psychotic cancer researcher, while unable to cure cancer could graft cancer dissected from one woman’s cancer onto another women’s breast and both women develop and die of cancer. And at the same time ‘Together we will beat cancer’ women in pink, as if revolutionaries of the 20th century, are chanting on the streets. More money moves into the coffers of cancer institutes, little kids eager to become scientists appear on TV – yess, they will work hard for many years earning peanuts until they become unemployable, while the bigass celebrities shimmy their bits on stage for big bucks. How fair and right is that? Why should I be helping to save the world like that? Get you priorities right, earthlings!

BTW, I am in shimmying training myself – it feels good!‘said harry

‘Woooing to the devil, harry. Where that anger coming from? You must be in love and rather frustrated’ Lorenzo is teasing harry.

‘Hmm.’ Said harry. ‘I am always in love with something, somebody or other. I was in love with a starling with a broken wing. I wished I could heal his wing but then he would fly away and never came back. It is a rather a big conundrum for me. The sated and overfed malicious black and ginger cruellas are chasing him around the garden. I wish I could kill them but then cat-lovers would crucify me for cruelty. That is the right kind of symbolism to explain cancer, don’t you think. Starling is the weakened clonal body and the cruellas are freshly activated cancer stem cells. We all have pool of good and bad stem cells, which are used to renew our organs. Every organ consists of many cells of predetermined fate. The good ones follow the predetermined rules and the bad ones do not. It is stress and aging that activates the bad ones. Aging is a natural and genetically predetermined process. The bad ones are activated all the time but forced to commit suicide, because the clonal organism detects non-self. Normally, the only time non-self is tolerated is for the purpose of reproduction (i.e. making babies). Any organism consists of many loops on a global and local scale (or feedback mechanisms) that feed from each other. Many loops are developmentally predetermined – i.e. some should only happen at blastocyst stage, for example. Cancer stem cells divide into one stem cell *whixh goes to sleep) and one proto-cancer, which divides and multiplies i.e. differentiates. In contrast to normal cells this differentiated cell is immortal and divides many times with many errors until it accumulates the right number of core LD or core LDs without the wide LD. Simply said – it separates clonal organism specific attractors from its own basins of attraction, creates chaos and from this chaos new order is molded. And, if all goes ‘well ’tumour’ is formed.’ Concluded harry

‘Good news, I saw starling flying and landing in the morning so my above outlined parabole is not valid anymore.’ Said harry to Charles I.

‘The question is why that differentiated proto-cancer cell does not commit suicide after pre-determined number of divisions.’ Said Charles I

‘Its fate is wrong.’ Said harry. ‘And we only learn about this when it succeeds in its run for freedom. I go on and on about the mechanism of this process in my intro. My favourite gene is the master key in this game of selfish and opportunistic (cancer cell) against altruistic and collaborative (clonal organism). ‘harry concluded.

‘Heyhey’ said Mr Skinny. ‘I can back you up, Harry. I have been studying stem cell all my research life and develop a method on how to trace cell lineages following cell divisions. We published last August (8/2016) that formation of proto-tumours is down cell fate errors. You had this idea before us Harry – your dissertation was submitted (i.e. published) in April and before us) and you also formulated it so brilliantly. Absolutely incredible! Socks up in the air for you and your brilliant achievements!’

‘Thanks Mr Skinny.’ Said Harry. ‘I have not read your paper in Nature yet because I have no access to this exclusive bulbar, where people funded with public purse deposit their achievements. Another excellent paper of yours is the one about the role of Notch signaling in proto-cancer development. It would be nice if I could contribute but you would throw my CV into a rubbish bin if I applied for any jobs with you. I am really sorry. ‘concluded harry.

‘I better stick to writing love sonnets to my imaginary admirers i.e. one starling with broken wing and sparrow-hawk, who has starlings with radio-transmitters for lunch.’ Said Harry. The starling mentioned above is now dead or moved out. 

Source code for lorenz: https://github.com/gboeing/pynamical
Inspiration in chaos: blog by Sofia Price https://devblog.bango.com/2017/07/12/software-imitates-life/ (those microservices are my LD units, not so  sure whether core or wide)