Sam's blog

Day 015 - The Human Brain Project: another brain simulation

Submitted by Sam on 5 June, 2011 - 00:51

The Human Brain Project, or HBP, is described as the successor to the Blue Brain Project. The HBP does what it says on the tin, explicitly aiming to simulate the complete human brain with as much biological detail as is technically possible. The HBP will pursue this goal by building a phased sequence of biophysical, phenomenological and abstract models at various resolutions and scales (from model brain regions, mesocircuits, to whole brain systems, or macrocircuits), starting with animals like rats and mice, progressing to cats and monkeys and finally to humans.

Like the Blue Brain Project, the HBP will be constantly comparing the properties of its model circuits against existing experimental data, ensuring wherever possible that their virtual brains corroborate with the 60,000 pages of neuroscientific research that are published every year. Unlike the Blue Brain Project, the project's computer engineers will be running multi-level simulations to reduce the overall computing requirements by simulating highly active neurons in great detail whilst modelling less active neurons with lower accuracy.

The scope of the HBP's roadmap reads like a transhumanist manifesto. Here are some of the juicy bits:

  • The project intends to develop its facility, tools and skill-sets to be able to model the brain of any animal, at any stage of its development, in any state of health or with any specific disease.
  • The later stages of the project make provision for computing requirements thousands of times more powerful than any in existence today.
  • The high-level mathematical theories of brain function will be able to combine with the technologies needed to create realistic simulations to create a new class of brain-like hardware devices and computer architectures.
  • These new information technologies will have the brain's capabilities to repair itself, to learn, and to be creative, utilizing neuromorphic circuits derived from the circuitry of the brain.
  • A brain simulation will provide insights into the basic causes of neurological diseases such as Alzheimer's, Parkinson's, autism and depression.
  • A virtual model will present a new platform for testing drugs, facilitating the creation of targeted drugs with fewer side-effects, and reducing our reliance on animal testing.

Day 014 - The Blue Brain Project

Submitted by Sam on 3 June, 2011 - 21:28

In his excellent 2008 interview with Seed Magazine, Henry Markram gave a fascinating tour of the Blue Brain Project, which pursues the humble mission of reverse-engineering the brain. Having looked at the principles of connectionism already, the reasoning behind the project should sound familiar. Here's what Markram had to say: “There is nothing inherently mysterious about the mind or anything it makes...Consciousness is just a massive amount of information being exchanged by trillions of brain cells. If you can precisely model that information, then I don’t know why you wouldn’t be able to generate a conscious mind.”

Since 2005 the Blue Brain Project has systematically constructed the foundations for a complete virtual human brain. The first step the project took was to simulate the neurons in a two-week old rat's cortical column, the smallest functional unit of the neocortex, which is believed to be responsible for high-level functions such as conscious thought and sensory perception. As basic units of the cortex, each cortical column seems to be assigned a discrete function – in a rat, for instance, a column is devoted to each whisker. A rat's cortical column is the size of a pinhead, has 10,000 neurons in 50 different types, joined by 108 synapses. Human cortical columns are very similar, but contain around 60,000 neurons.

The team automated the process of analysing the genetic expression of real rat neurons using a patch-clamp robot, and used the data from their experiments to create a precise map of the ion channels in the rat's neurons. They fed this information back into their Blue Brain simulation, which runs on an IBM BlueGene/L supercomputer. Throughout the process, the researchers were able to continually test their model against real neural activity in a real live rat, fine-tuning their simulation against the performance of the real thing.

Using this data the team were able to assemble a three-dimensional model that precisely simulated the neocortical column of their two-week-old rat. When stimulated with the same sort of electrical stimulation that a newborn rat would actually experience, the model reacted just like a real neural circuit, with clusters of connected neurons firing in close synchrony, spontaneously wiring themselves into meaningful patterns.

The generated model's behaviour corroborates results observed from years of neuroscientific experiments, and will be able to serve as a building block for a full-scale simulation of the human brain. It seems that all that is holding the project back now is computational power. The team estimate that a supercomputer capable of processing 500 petabytes of data would be required to run the full simulation of the human brain. This phenomenal computational requirement is needed because there are 100 billion neurons to model, and each one requires 400 independent simulations (and the power of a laptop computer) to accurately replicate the complex chemical activity of its biological counterpart.

One of the most exciting implications of Blue Brain, and the subject of Markram's TED talk, is its potential ability to allow us to step into another brain's reality. Markram has said that “there’s no reason why you can’t get inside Blue Brain ... Once we can model a brain, we should be able to model what every brain makes. We should be able to experience the experiences of another mind.” In order to project a brain's interior experience into perceptual space, the code that generates the electrical objects of neural activity need to be deciphered – a challenge that Markram insists is not impossible. If Markram's projections are true, it will one day be possible to see the world through someone else's eyes.

Day 013 - Simulating the brain

Submitted by Sam on 3 June, 2011 - 00:00

Henry Markram, like Sebastian Seung, is a neuroscientist working towards a connectionist model of the brain. Like Seung, Markram is convinced that it is fundamentally possible to fully simulate the human brain, and that the only limiting factor in doing so is research funding: “it's not a question of years, it's one of dollars” 1. Like Seung, Markram also gave a TED talk about his work modelling the brain, which is linked below.

In his talk, Markram suggests that our brains project a 'perceptual bubble' around us, created from thousands of decisions and inferences that we subconsciously make: 99% of what we 'see' is what we infer, not what comes through our eyes. The question which motivates Markram's talk and which animates his efforts to model the brain is, “can the brain build such a perception?” - does it have the capability to generate it's own reality?

Markram is director of a supercomputing project, Blue Brain, which aims to answer this question. We'll have a look at his methods and progress tomorrow.

Day 012 - Connectionist theories of mind

Submitted by Sam on 1 June, 2011 - 23:32

Yesterday's video, Untangling the brain ended on an optimistic note for the future of connectomics, projecting that neural maps might perhaps “one day reveal how a tangled mess of billions of cells enables us to see, to dream, and to study the brain as scientists, and how to repair it when it goes wrong.” MIT's Sebastian Seung shares this optimism, believing that we are our connectome, and that one day we will have the technologies to test his theory “I am my connectome”, which he lays out in his 2010 TED talk below.

In essence, Seung and other connectionist neuroscientists theorize that our personality and memories are encoded in full by our neural connections. Unlike our genome, which we possess in its entirety from birth and which changes only by random mutation over our lifetime, our connectome must be constantly changing as experiences and memories are encoded in to the neural pathways of the brain. This part of the theory is substantiated by the decades of evidence for the neuroplasticity of the brain, which shows that the brain is able to change both anatomically and physiologically as the strength of connections between neural units are changed, and synapses are created and deleted. The only real uncertainty in Seung's theory is whether these changes are indeed the basis of memory and the encoding of experience and personality.

If they are, and memories are indeed stored as chains of synaptic connections, as sequences of neural activity which are activated in the brain during memory recall, then it will be possible to represent any mental state through a numeric description of activation values of the neural units in the brain. Memories, thoughts and personalities will be able to be expressed as n-dimensional vectors.

Day 011 - Towards a circuit diagram of the brain

Submitted by Sam on 31 May, 2011 - 22:54

Neuron cells are so small that they cannot be seen clearly with a light microscope, as the finest branches of their tree-like structures are less than a tenth of a micron in diameter and so are smaller than the wavelength of visible light. Neurons are so small and so highly entangled with each other that they can only be seen with an electron microscope. Their tiny size and dense interconnectedness makes the work of mapping a connectome of even the simplest nervous system an exceptionally difficult task.

It took over a decade for scientists to map the 302 cells that make up the nervous system of c. elegans, and despite over a quarter-century of technological progress in imaging and automation techniques the process is still painstakingly manual today. Just as our friend the c. elegans worm was chopped into 50nm slices, photographed and reconstructed by hand from the resultant 8000 prints 1, so scientists in pursuit of a connectome today must combine knife and microscope to generate a three-dimensional structure from a sequence of two-dimensional images. The very recently released video below provides a very nice visualization of how this process was used by researchers at both the Max-Planck Institute for Medical Research and at Harvard, as well as an extremely concise overview of the scope of connectomics as a whole.

As the research of neural wiring is still very much in its infancy, the algorithms that are currently available for automating the tracing of neural pathways are still far from perfect, making classification mistakes which might merge two neurones into one, or split one into two. Humans are currently faced with an incredible amount of manual work just to trace all of the branches in a cubic-millimetre of neural tissue. However, in what will become a motif of this blog, scientists like Sebastian Seung, Professor of Computational Neuroscience at MIT, are optimistic that advances in our technological capabilities will one day allow researchers to overcome these technical problems. Once we have robust pattern-recognition algorithms, Seung believes that we will be ready to find whole connectomes, starting with simple nervous systems and scaling up to larger brains as our technical abilities grow 2.

  • 1. White, J. G., E. Southgate, J. N. Thomson, and S. Brenner. "The Structure of the Nervous System of the Nematode Caenorhabditis Elegans." Philosophical Transactions of the Royal Society B: Biological Sciences 314.1165 (1986)
  • 2. Seung, Sebastian. "Connectomics - Dana Foundation." Brain and Brain Research Information - Dana Foundation. Web. 31 May 2011. http://www.dana.org/news/cerebrum/detail.aspx?id=13758.

Day 010 - Connectomics

Submitted by Sam on 30 May, 2011 - 22:05

A complete map of the totality of a brain's neural connections is called a connectome. The term was coined in 2005 in anticipation of a new field of neuroscience – connectomics – being driven into existence through technological advances that facilitate the tracing of neural wiring in brains. There is an intentional similarity between the words connectome and genome (the entirety of an organism's hereditary genetic material) which indicates the potential significance of this emerging field.

Appropriately, The Human Connectome Project bears a strong resemblances to The Human Genome Project, which completed its mission to produce a complete sequence of human DNA in 2003. With the successful description of our friend c. elegans' connectome as a precedent, The HCP aims to produce a complete structural description of the human brain by using imaging techniques to comprehensively map the circuitry of 1200 healthy adult's brains. It is a multi-million dollar research project of exceptional scale.

The project is consequently faced with many of the criticisms that were levelled at The Human Genome Project, principally concerns about its ability to achieve results in a realistic time frame. Regardless of the viability of the project's deadlines, the potential consequences of successfully mapping a human connectome are manifestly too important not to pursue. A complete schematic of the wiring of our brains would help us understand diseases like autism and schizophrenia, and would give us critical insight into the foundations of our consciousness, our intelligence, our memory and our personality.

Day 009 - Mapping the brain

Submitted by Sam on 29 May, 2011 - 22:38

Comprised of over one-hundred billion neurones, the neuronal network of the human brain is quite something. The project to trace the brain's complete circuit is desperately difficult, but it isn't desperately complicated. Morphologically, our brain isn't fundamentally different from the brains of much simpler organisms, which are also constructed from the same basic components as our brains are: neurones joined by synaptic junctions.

In the 1980s, scientists completely mapped the neural network of the nematode worm, c. elegans, using techniques which can be used to trace the wiring of any brain comprised of neurones. Using electron micrographs of serial sections of the worm, the team created a complete reconstruction of the 302 neurons that form the 7000 synapses of the adult hermaphrodite, which was chosen for the simplicity and consistency of its nervous system's construction1.

Whilst a neuronal map doesn't provide us with an understanding of how the network itself functions, it does serve as a crucial first-step towards a working replica of the human brain.

  • 1. White, J.G., Southgate, E., Thomson, J.N., and Brenner, S. (1986). The structure of the nervous system of the nematode Caenorhabditis elegans

Day 008 - A top-down approach

Submitted by Sam on 28 May, 2011 - 22:35

The past week has been a desperate uphill struggle to find bottom-up ways of looking at the universe. It has resulted in an unrelentingly tedious stream of pseudo-philosophical rot, so let's put the hypothetical basic principles of the universe to bed for now, and see what metaphysics looks like from a top-down perspective. Here we go.

The common or garden human brain is a fabulously complex network of billions of nerve cells called neurons which transmit information between each other using electrical and chemical signalling. Neurons acquaint with each other at junctions called synapses, where they exchange information using electrochemical gateways. A single neuron may branch many times, terminating in many synaptic junctions to create a massively interconnected and interdependent circuit.

The neuronal topography of each of our brains is utterly unique, as no neurone in the brain is the same as another, and no two brains contain neurones connected in exactly the same way – even identical twins are uniquely wired. The number of possible connections, configurations and orientations of neurons in the human brain is almost unmanageably large, even though each brain follows a fundamentally similar design pattern.

With the possibility that all of our thoughts, hopes and dreams are carried, processed and encoded by the brain's neuronal network, the motivation to transcribe and decipher these neuronal pathways in their totality is huge. It's a correspondingly massive task, but advances in non-invasive neuroimaging have made the possibility of a comprehensive map of the neuronal structure of the human brain a possibility. The Human Connectome Project is committed to describing the brain circuitry of 1200 healthy adults, providing us with the outlines of a blueprint for a functional human brain.

Day 007 - Trying to make it work

Submitted by Sam on 28 May, 2011 - 01:26

In order to grant us the autonomy that we should like, we have to assume that there is something special about the way we think. To allow us access to the dictionary definition of free will, our thought processes would need to be essentially distinct from the rest of the universe. Our thoughts must then effectively derive from their own system, which must be neither determinable in principle nor random, for the reasons we have seen previously.

In a random system, there are inscrutable events where, to use a crude example, an atom with state 'zero' suddenly changes to state 'one' with no precedent and under the guidance of no law whatsoever. In our true free-will system, a similar level of inscrutability is present, but here the zero changes to a one because the person thinking wills it to.1 This very special super-power ascribes humans the ability to change the rules of their thinking-system at will.

But here there arises the problem of precedence, and the system breaks down into a chicken-or-egg paradox. How can the desire to flip a zero to a one manifest itself without the instruction itself being either encoded by the system, or randomly generated?

  • 1. The person wouldn't be willing on an atom by atom basis of course!

Day 006 - A third option

Submitted by Sam on 27 May, 2011 - 01:38

From what we've seen so far, it seems that we live either in a system in which our thoughts and actions are either fully prescribed and predictable, or we live in a world where truly random variables devalue the meaning of everything that makes us human.

In a determined system, if I were so bold as to align atoms in my brain to ask myself a question, the universe's procedural set of rules would ensure that only one truly possible answer could ever resolve, despite the illusion of multiple choice that might manifest in my consciousness.

In a non-determined system, fundamental aspects of the atomic (or sub-atomic) interaction of the thought-making components of my brain are left to chance, and so their subsequent states occur probabilistically. Randomness kicks in at some level to take the decision away from me, leaving parts of the decision-process to a metaphorical coin-toss.

Note that a conscious indication of the loss of autonomy is apparent to me in neither situation.

These are both grossly unpalatable options, so let's conjure a third, our get out of jail free card. We want this option to give us true free will, and the ability to exercise this free will in a meaningful way. It must therefore be an anthropocentric mixture of unpredictability and determinism. It must allow for our thought-making processes to operate beyond the predictability of rules at all, yet simultaneously remain outside of chance and random interference. It must allow for a fully-determined world beyond our thoughts so that the causes and effects of our actions develop logically from one another, free from the disruption of random events which would otherwise make our internal choices meaningless.

Option three requires a truly unpredictable process but requires this process to have no random elements to it. This is a logically unsustainable requirement unless we grant some anomalous powers to our thought-making apparatus.

I shall have to dream up these powers for tomorrow's exciting edition.

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