The NeuroGene Project

Gene

Genes make Brains and Brains make decisions. We humans are taking decisions every day and they are these genetic code APIs that are sent over the neural network to the brain at a speed much faster than the speed of light leading to decisions. And if the decision is wrong, there is a feed-backward connection from the brain to the Genes, so our neurons are changing as well as our genes every single day.

Going a level up, there are common behaviours or characters that are shared between humans so these characters are genetically encoded and distributed among multiple brain processors in the genetic pool (like Erlang processors in distributed systems).

But how does an organism emerges from a single cell? It’s utterly intriguing how unordered atoms group themselves to form the initial cell in the first place and how the cell gets copied and replicated in a structured pattern to form the 37 trillion cells of our body. The human cell is made up of water 70%, proteins 15%,Carbohydrates 2%, Lipids 2%, Ions 4%, RNA 6% and DNA 1%. It’s fascinating how much water we have in our cells and what is more fascinating is that 1% of DNA carries the genetic code for over 3 Million years of our existence. A DNA molecule is a long chain of building blocks, small molecules called nucleotides. Just as protein molecules are chains of amino acids, so DNA molecules are chains of nucleotides. It consists of 2 pair of nucleotide chains twisted together to form the double helix. The DNA code is a set of programming instructions (API Calls) distributed among our thousand million million cells of human body and instead of 2 digits (0 or 1) as in computer systems, it utilizes 4 nucleotides (A, T, C, G). These APIs are translated into amino acids to implement the different kinds of proteins that make our body. How do these 4 nucleotides determine features like the colour of the eye or the height for example? A gene encodes information to build proteins and the proteins enable functions of the body. And how the gene encode information to build proteins? A protein is created from 20 amino acids and DNA are made of 4 nucleotides so the fuProteins Functionnction should be 43 , 3 bases of DNA had to specify 1 amino acid in protein. 2nd the proteins need to be synthesized within the cell by ribosomes and that’s why DNA are translated to messenger RNA first and then encoded into proteins. DNA replication mechanism is by far the most important process in building human bodies where the strands are separated by DNA helicase first and then bind to DNA primase and its interesting how DNA polymerase do the proofreading to detect and correct replication errors. DNA polymerase partnership with DNA synthesis lays the base for Polymerase chain reaction PCR process which allows amplifying any DNA sequence by DNA polymerase and then the sequences are fragmented by restriction enzymes into small pieces and separated by length using Gel Electrophoresis.

Mathematically speaking, the human genome is ~ 3 Billion base pairs with 46 chromosomes, each chromosome has millions of base pairs – each of 2nm diameter and if you stretch out the entire human genome, it would be long enough to go from the earth to the sun and back 300 times. So all of this need to be packed in our tiny cells and that’s the process of DNA packaging – DNA wound around histones, histones (+vely charged) main role is to pack DNA into little groups of 8 called nucleosome. And they packaged- packaged- packaged, condensed-condensed-condensed to form chromosomes.

Moving forward, using data analytics to analyse the genome data come with a lot of challenges; storing the data is one of the most challenge – Just imagine only 1g of DNA holds 450 exabytes of data more than all the data processed by Google. Also how information are stored in the DNA strands place another challenge for how to convert the 4 nucleotides base A, T, C, G into digits 1 and 0 and perhaps come up with new structure for representing information based on 4 digits rather than 2.

Gene relation

Recently, I was working on analyzing gene-disease association data from the world bank and have run the data on graph database to see correlations and associations as shown below – the relation is many to 1 most of the time, many genes contribute to certain disease and I would assume that many genes contribute to certain features of the human being and its not 1:1 relationship.

 

Gene Disease Neo4j

My favorite quote on the subject:

” Improved environment and education may better the generation already born. Improved blood will better every generation to come …… Herbert Walter

Second comes the Brain with its most fascinating architecture – bigger than all the cosmos and planets combined.

Map4

So how big is the brain? In this 10*10 cm³ we have 1011  neurons and 1014 1015 synapses. The design secret of the brain is diversity, every neuron inside my brain is different and it took 11 billion years to build a brain with billions of ASIC processors. The synaptical network of the brain is much much bigger than the internet network and uses smart OSPF routes all the time. But it’s not only that, there are Glia cells in the background and these cells don’t communicate using electrical or synaptical action potentials but they communicate through calcium ions. What are these cells doing up there? are they controlling the synaptic transmissions between neurons? are they communicating with the neurons during decision making? The answer is I don’t know yet and discovered science doesn’t know too – what we know is that there is this thin 2mm layer in the brain named Neocortex that constitute 60% of the volume of the brain, it receives inputs from the thalamus through the feedforward network, do processing through the different layers and feedbackward to the thalamus but do we really understand the language of the brain?          Neocortex

Thalamus-Cortex

The Engineering Architecture of the Brain 

Note:This is personal imagination and could be wrong or right.

As you see in the architecture, I positioned the Amygdala in the centre of the brain. Although it’s a small part of the big brain, but it’s the most important as it receives information from our 5 senses that were defined by Aristotle and responds accordingly. This Amygdala is coded differently between humans and the embedded code can change over time due to new experiences. There is a very complicated system in the background that is processing the code and taking decisions, this system is not only composed of the amygdala but also the neocortex. Why I am studying neuroscience today and why I did engineering yesterday? The answers lie in the Neocortex, the frontal cortex around the limbic system, and the limbic system itself that includes the Amygdala.

Article

Trying to understand how the brain works, I will start first with the basics of Neurons and synapses. Neurons are discrete cells, a leaky bag of charged liquid made of dendrites that receive inputs from other neurons. These dendrites lead to cell body which sustains the life of the cell and contains its DNA. Information flows from the dendrites to the axon via the cell body as shown in the architecture. The Ionic channels allow ions to path through, which give rise to action potential and spikes. Brain information is stored in the physical and chemical structure of neurons and synapses. Neurons don’t use LinkedIn to connect with each other, they use synapses. When the dendrite receives a lot of excitatory signals, it will fire a signal through the axon to the dendrite of another neuron but it doesn’t touch the dendrite because of the synapse that separates neurons from each other The synapses are the basis for memory and learning in the brain, all the memories and learning are stored in the synapses. The synapse release neuro-transmitter which causes ionic channels to open or close which in turn change the membrane potential.  So memories are stored in the synapse but what about perceptions? This is beyond the synapse; it’s a network of neurons that give rise to perception, behaviour and consciousness.

Third, we get to the behaviour and decision making. To get a glimpse of how the brain generates behaviour, let’s look at the computational models. There are three models used in computational neuroscience: The descriptive model for characterizing what nervous system do through encoding and decoding, the mechanistic model for determining how they function by simulating a network of neurons and the interpretive models for understanding why do brain circuits operate the way they do. In all these models, the receptive field is the base. When we look at an object, the information from the retina is passed to the Lateral Geniculate Nucleus LGN and this passes information to the back of the brain to an area called the primary visual cortex V1. The mechanistic model shows how do receptive fields (LGN cells) constructed using the neural circuitry of the visual cortex to form V1 cell and the interpretive model shows why are the receptive fields in V1 shaped in specific way. After knowing the what, how and why, we can go further to look at how neurons are connected to form recurrent network using Eigen vectors and Eigen values and then how these connections can be adapted using synaptic plasticity allowing the brain to learn about the world from its inputs and change the brain map accordingly.

After learning how the brain generates behavior, we need to understand the neurotransmitters. When the neuron fires an electric signal, it causes a release of neurotransmitter, a chemical that travels throughout the brain and binds to receptors that are attached to other neurons. I will start by the Noradrenaline, the Neuro transmitter responsible for the sympathetic nervous system. It controls the heart, vision lungs, vessels every single function in our body. Now the connection between prefrontal cortex and hippocampus is a fibre optic of noradrenaline neurons in the locus coeruleus deep inside the skull. Testosterone, on the other hand, is associated with aggressiveness and pursuit of dominance. Oxytocin is released from the pituitary gland that secretes prolactin and this affects fear. Vasopressin, on the other hand, affects relationship. Finally, the Dopamine which plays an important role in the reward motivated behavior, and Serotonin, a neurotransmitter that affects mood, that’s why antidepressant medications like Prozac and Zoloft act on serotonin receptors. People with a variant of dopamine regulating gene DRD4 take more risks in life than people a variant of serotonin regulating gene SERT.

More about dopamine – Looking at the visual system, the network of neurons in the prefrontal cortex is the basic for paying attention and they are sensitive to dopamine only. When dopamine is released, it unlocks these neurons which they start firing tiny electrical impulses that stimulate other neurons in their network.  Taking the auditory system, I went to a rock festival for one of the best guitar players kurt vile, I liked some of his plays and didn’t like the others; so how the brain distinguish between consonant and dissonant sounds? When the sound comes to the eardrum, it will be split into 2 processing circuits, 1 circuit that process speech which decompose the signal to identify vowels and consonants that make the words, and 2nd circuit that process music and separately analyse pitch, timbre and rhythm; the 2 signals connect with the frontal lobe that do temporal pattern matching like in functional programming.

So what’s next? What we know about the brain is very limited and am not sure if the scientific understanding of neurons and synapses is correct. Just imagine there are 500 synapses in 1 red blood cell and there are 100s of billion cells; So you have billions of billions of synapses. To simulate one brain only, it needs trillions of computers and that’s mathematically impossible. Moreover, every brain is different and neurons in one brain are different than neurons in another. Adding more complexity, the brain is only 15% neurons and most of these are in the cerebellum not the cerebrum, 85% of the cells in the brain don’t use synapses (no dendrites, no axons) to communicate, don’t make electrical impulses, and these cells communicate with other cells that have neurons and use synapses. On a scale from 1 to 10, we are still at level 1 of brain discovery and it might take 10,000 more years to get an answer of how exactly the connections are built in this almond shape structure that’s named brain and that we carry with us every day.

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