Biology, Computer Science, Geography, Group, In the Media, Milestones, Murderous Maths, Notes on everyday life, Physics, Trips

World Science Scholars Feature Simon’s visit to CERN in a newsletter. The current course is about neurons. Reading Stephen Wolfram.

Simon’s September visit to CERN has been featured in a World Science Scholars newsletter:

Here’s our update on the World Science Scholars program. Simon has finished the first bootcamp course on the theory and quantum mechanics by one of program’s founders, string theorist Professor Brian Greene and has taken part in three live sessions: with Professor Brian Greene, Professor Justin Khoury (dark matter research, alternatives to the inflationary paradigm, such as the Ekpyrotic Universe), and Professor Barry Barish (one of the leading experts in gravitational waves and particle detectors; won the Nobel Prize in Physics along with Rainer Weiss and Kip Thorne “for decisive contributions to the LIGO detector and the observation of gravitational waves”).

September 2019: Simon at a hotel room in Geneva taking pat in his first WSS live session, with Professor Brian Greene
September 2019: screenshot from Professor Brian Greene’s course module on quantum physics

At the moment, there isn’t much going on. Simon is following the second course offered by the program, at his own pace. It’s a course about neurology and neurological statistics by Professor Suzana Herculano-Houzel and is called “Big Brains, Small Brains: The Conundrum of Comparing Brains and Intelligence”. The course is compiled from Professor Herculano-Houzel’s presentations made at the World Science Festival so it doesn’t seem to have been recorded specifically for the scholars, like Professor Brian Greene’s course was.

Professor Herculano-Houzel has made “brain soup” (also called “isotropic fractionator”) out of dozens of animal species and has counted exactly how many neurons different brains are made of. Contrary to what Simon saw in Professor Greene’s course (mainly already familiar stuff as both relativity theory and quantum mechanics have been within his area of interest for quite some time), most of the material in this second course is very new to him. And possibly also less exciting. Although what helps is the mathematical way in which the data is presented. After all, the World Science Scholars program is about interdisciplinary themes that are intertwined with mathematical thinking.

Screenshots of the course’s quizzes. Simon has learned about scale invariance, the number of neurons in the human brain, allometric and isometric scaling relationships.

Another mathematical example: in Professor Herculano-Houzel’s course on brains we have witnessed nested patterns, as if they escaped from Stephen Wolfram’s book we’re reading now.

screenshot from the course by Professor Herculano-Houzel

Simon has also contributed to the discussion pages, trying out an experiment where paper surface represented cerebral cortex:

The top paper represents the cerebral cortex of a smaller animal. Cerebral cortex follows the same physical laws when folding is applied.

Simon: “Humans are not outliers because they’re outliers, they are outliers because there’s a hidden variable”.

screenshot from Professor Herculano-Houzel’s course: after colour has been added to the plot, the patterns reveal themselves

Simon is looking forward to Stephen Wolfram’s course (that he is recording for world science scholars) and, of course, to the live sessions with him. The information that Stephen Wolfram will be the next lecturer has stimulated Simon to dive deep into his writings (we are already nearly 400 pages through his “bible” A New Kind of Science) and sparked a renewed and more profound understanding of cellular automata and Turing machines and of ways to connect those to our observations in nature. I’m pretty sure this is just the beginning.

It’s amazing to observe how quickly Simon grasps the concepts described in A New Kind of Science; on several occasions he has tried to recreate the examples he read about the night before.

Simon playing around in Wolfram Mathematica, after reading about minor changes to the initial conditions of an idealised version of the kneading process
Simon working out a “study plan” for his Chinese lessons using a network system model he saw in Stephen Wolfram’s book “A New Kind of Science”
Biology, Murderous Maths

The All Common Ancestors Generation

This project is a simulation of how many people can stem from the same ancestor, something Simon has learned from James Grime’s “Every Baby is a Royal Baby” video on Numberphile. In this simplified version, there’re only 6 people per generation. Simon was throwing two dice to determine who the two parents were for every person (in the case when both dice came out to be the same number, this was considered “virgin birth” or simply that the father had come from outside the limited sample Simon was working with).

the present generation
Simon marking who the children of a person were in pink pencil
Some parents don’t have the digits corresponding to their children written next to them, but letters N and E: N means that that person from the parent generation had no children and is therefore related to no one from the future generations; E on the conrrary, means that that person “has been busy” and is related to everyone in the next generation!
identifying the most recent common ancestor generation and the identical ancestors generation
the all common ancestors generation
Biology, Coding, Java, JavaScript, Milestones, Simon makes gamez, Simon's Own Code

Simon has created an “immortal” organism?

The organism is the green triangle on the left

Simon opened up a genetic algorithm game he built about two years ago and made a fascinating discovery: one of the organisms seems to have become immortal! Simon has called his discovery “The Everlasting Vehicle” and saved the vehicle’s DNA.

Links to the game on GiHub:
Original code: https://github.com/simon-tiger/steering-behaviors-evolution
p5.js version: https://simon-tiger.github.io/Game_SteeringBehaviorsEvolution/SteeringBehaviours_EvolutionGame_p5/

Simon writes:
The last time I ran the program is a couple of hours ago. Everything died out, except for one vehicle.

Stats
I have programmed this with a genetic algorithm. They have a DNA with 4 genes.

Attraction/Repulsion to food
Attraction/Repulsion to poison
How far it can see food
How far it can see poison
They also have a health, which goes down over time. If they eat food, then their health goes up, if they eat poison, then their health suddenly goes down. A good health is 1, and a bad one is 0.

So what was The Everlasting Vehicle’s DNA and health?

Property Value
Attraction/Repulsion to food 1.9958444373034823
Attraction/Repulsion to poison 1.3554737395594456
How far it can see food 53.31017416626768
How far it can see poison 23.33902221893798
Average health ~397
So it attracts to poison, yet its health is approximately 397 times bigger than a very good health! And better yet, it even lasted for a couple of hours so far!!!

Credits:
Inspired by Daniel Shiffman’s Evolutionary Steering Behaviors Coding Challenge
Link to the Challenge: https://www.youtube.com/watch?v=flxOkx0yLrY

Biology, chemistry, Math Riddles, Milestones, Murderous Maths, Physics

Bayes’ Theorem

Bayes’s Theorem calculates the probability of an event based upon the conditions that might be relevant to the event and is widely used to test the precision of medical tests and drugs efficacy.

Simon explains Bayes’ Theorem to Dad. To illustrate the theorem, he loves using the math riddle he first saw on the Veritasium channel, about someone getting positive results on a rare disease test: The test has a precision rate of 99% and it is also known that the disease occurrence rate is 1/1000. What is the probability that the person tested positively really has the disease? (Answer: 11/1000 or 9%).

Biology, Milestones, Notes on everyday life, Physics, Simon's sketch book

Electromagnetic Spectrum and the Opponent-process Theory

Simon has been fascinated about the Opponent-process theory (suggesting that color perception is controlled by the activity of three opponent systems, three independent receptor types which all have opposing pairs: white and black, blue and yellow, and red and green). He has been complaining that all the papers on Opponent-process Theory he has managed to find online were too superficial.

Biology, chemistry, Crafty, Geometry Joys, Milestones, Notes on everyday life, Physics, Together with sis

Molecules

Simon is seriously enjoying his new Molymod chemistry modeling sets and has been obsessing about which set contains what atoms and bonds.

Alcohol (Ethanol):

Hurray! We have just built 7,333333333333 x 10^-9 of the human DNA:

Glucose

Some like the football, Simon plays with the buckyball, or Buckminsterfullerine, made up of 60 carbon atoms:

Biology, Physics, Simon teaching, Together with sis

Microstructures Interfering With Light

What looks like strange planets in dark space are actually glimpses of the microstructures forming the Giant Blue Morpho’s wings, as seen through a microscope. Simon told me about how a Blue Morpho’s wings aren’t actually blue (have no blue pigment) but appear blue as a result of a physical phenomenon called structural coloration — microstructures interfering with light. This is almost the same phenomenon as iridescence (making a surface appear to change colours as the observer’s angle of view or the illumination angle changes, think of the soap film in a bubble).

We had found Blue Morpho’s wings in the street about half a year ago. Someone threw a small butterfly collection away — several butterflies pinned to a stick. It looked very cruel and we would have never killed a Blue Morpho for the sake of an experiment, but since we stumbled upon such a rare treasure, we picked up one wing and stored it in a book.

Biology, Crafty, history, Together with sis

Building dinos and looking them up in the encyclopedia

Although Simon doesn’t have the Magformers Dinosaur Set, he does have all the pieces (he collects the set using the pieces from other sets). It’s great fun to be able to look up the dinos and the instructions in the Magformers online pdf books and bring them back to life:

Schermafbeelding 2018-10-15 om 12.13.56

Schermafbeelding 2018-10-15 om 12.11.24

Schermafbeelding 2018-10-15 om 12.06.47

Schermafbeelding 2018-10-15 om 12.05.28

We also read up on how these dinos lived in the encyclopaedias.

Biology, Coding, Java, Milestones, Murderous Maths, Simon's Own Code

Barnsley Fern in Processing

Simon used an algorithm that applies transformations randomly, with some transformations more likely to be picked. The result is a stunning fern leaf pattern. Amazing how such beauty can be born from randomness. Simon’s code on GitHub: https://github.com/simon-tiger/barnsley_fern

 

Inspired by a math video on Numberphile about Chaos Game.