The Amazing Brain Research and Supercomputing

Nages Sislack, the International Supercomputing Conference (ISC) Public Relation Director opened my eyes about the Human Brain Project.often called the Blue Brain Project  She interviewed., the project leader Henry Markram, in preparation for 'Supercomputing & the Human Brain Project", which will be held on Tuesday, June 18 in Leipzig ISC'13

Nages Sislack, Public Relations ISC

The Intense World Theory on Autism

Before going into details on why the brain research exploded almost overnight, I noticed that prof. Markram and his wife Kamila Markram - a well known brain researcher as well - are parents of autistic children. This experience motivated them  to extraordinary achievements. In 2010 they published  The intense world theory - a unifying theory of the neurobiology of autism:

... the Intense World Theory predicts that severely autistic people that cannot speak or interact at all have locked up abilities even greater than savants. In other words, those autists classified as severely mentally retarded by the psychiatrist, may be the greatest savants of all. 

Dr. Kamila Markram

 we will learn how valuable the autistic community is for society. We will adapt the planet to embrace rather than lockup autistic people. Normal people guess at the world, while autists process information completely, comprehensively. This feature would not be good for survival in the jungle, but in human society, we can nurture these individuals and they can make a fantastic contribution to society. We will begin special compensation to families with autistic children as if they are potential Olympic athletes of the world. 

This is music to my ears. Trying to solve the autism mystery from a total  different point of view, started it the most important scientific project in the 21st century so far.

$1.3 Billions in funding in Europe and $3 billions funding proposed in US by Obama Administration:

To add to the brain-mapping mix, President Obama in April announced the launch of an initiative called Brain (commonly referred to as the Brain Activity Map), which he hopes Congress will make possible with a $3 billion NIH budget. (To start, Obama is pledging $100 million of his 2014 budget.)

This adds to the 1.3 Billions Blue Mind has in Europe. But Wired Magazine is cynical:

For Markram, the American plan is just grist for his billion-euro mill. “The Brain Activity Map and other projects are focused on generating more data,” he writes. “The Human Brain Project is about data integration.” In other words, from his exalted perspective, the NIH and President Obama are just a bunch of postdocs ready to work for him.

Makram worked at NIH and everybody knows him there. Although the project has its' share of detractors like  John Horgan in Scientific American

 This finding bolsters the argument that the Big Brain Projects–by funneling precious resources toward paradigms supported by flimsy findings–are premature.

Luddites from two centuries in England ago re-surfaced in America. .Horgan  is a teacher at Stevens Institute of Technology (whatever that is)  and the author of four books, including The End of Science. Oh well...

The Blue Brain Project: Neuroscience, Medicine and Supercomputing

There is so much written on the Internet and I wanted to extract in a nutshell, why Professor Markram believes the brain could be simulated in a computer by 2020. In his opinion, we are stuck with several outmoded paradigms of thought. All quotes were from a 2009  interview in Discovery magazine

The first is related to how the brain represents information, what I call an action-potential paradigm. It’s a spike-based paradigm. Neurons generate spikes of activity. You can think of these spikes as digital: zeros and ones. Individual spikes do not have enough information to represent perceptions. The current view of perception is based on analyzing these zeros and ones and trying to decompose or reverse engineer the representation that these zeros and ones capture. But I think that the zeros and ones—the information generated or emitted by single neurons—are a reflection of perception, not perception itself.

 This is the first Aha! The other big misconception is memory:

For 50 years we’ve been thinking of memory, despite all evidence to the contrary, as where you imprint changes in the brain. You go to your synapses, you go to your neurons, and you change them when you remember something. And then you’ve got to protect those changes. It’s an imprint. It’s called an engram. Hundreds of scientists have been chasing this engram. Where is the print of memory in the brain? They think it’s like a scar, a mark. This is one of the most fundamental mistakes in neuroscience. And the reason why I say it’s a mistake is simple. All evidence indicates that the neuron does not reset. The synapses do not reset. They are always different. They’re changing every millisecond. Your brain today is very, very different from what it was when you were 10 years old, and yet you may have profound memories from when you were 10. What has to be answered in neuroscience is this: How do you remember something from long ago when your brain now is actually different?

In our view, the idea that memory is held in the brain the same way it is held in a computer is fundamentally wrong.

So this is not a simulation in our preconceived idea an engineering simulation.

You needed an entire, very powerful computer to run that simulation of one neuron. You needed the whole process. Of course, today computers are a little more powerful, and I can run a simulation of 100 neurons. But there’s really no point in doing a 100-neuron simulation. The reason is simple: A neuron lives in an environment. It receives thousands of inputs. So actually you need to make a quantum leap from one neuron to 10,000 neurons. You need to make that leap into what we call a microcircuit. A circuit of five neurons is not what the mammalian brain is made up of. To simulate the neurocircuitry that is creating the mammalian brain, you need to make a quantum jump in complexity. You need at least 10,000 computers to do that. And that’s what Blue Gene is—16,000 processors squeezed into a space the size of four refrigerators. It was important for us to have that many processors, because on each one we’ve got 1,000 neurons. The processors themselves did not have to be extremely powerful. They just needed enough memory to hold the neurons.

Henry Markham is featured TED speaker, He says:

And we've got the mathematics to describe this process. So we can describe the communication between the neurons. There literally are only a handful of equations that you need to simulate the activity of the neocortex. But what you do need is a very big computer. And in fact you need one laptop to do all the calculations just for one neuron. So you need 10,000 laptops. So where do you go? You go to IBM, and you get a supercomputer, because they know how to take 10,000 laptops and put it into the size of a refrigerator. So now we have this Blue Gene supercomputer. We can load up all the neurons, each one on to its processor, and fire it up, and see what happens. Take the magic carpet for a ride. 

 I noticed these   incredulous  comments

Apr 4 2013: Hello I have a question. If you can simulate 10 000 neurons with a supercomputer now, if you follow Moore's law you will be able to simulate 5 120 000 neurons in 10 years time. The brain has 86 billion neurons.

How do you expect to achieve simulation of all of them?

The answer came from another reader:

 May 25 2013: with 168 super computers. Which might sound crazy but isn't that the idea with cloud computing? Grant it we would then potentially have a consciousness on the Internet which if we go by terminator is a bad thing. However it should be a consciousness equivalent to only 1 human which doesn't sound so bad.

In 2009, we have not discovered yet the Higgs particle using CERN collaborative computing involving over 150 data centers in the world based on the collaborative computing technology developed by Prof. Miron Livny from University of Wisconsin, Madision. It is interesting to know that both Henry Markram and Miron Livny graduated from Weizmann Institute of Science.

Helping Medicine

Quote:

...there’s not a single neurological disease today in which anybody knows what is malfunctioning in this circuit—which pathway, which synapse, which neuron, which receptor. Doctors don’t even know this for a single drug—I mean, this is a multibillion-dollar industry!—that they’re giving for Parkinson’s disease, for depression, schizophrenia, attention deficit, autism, dementia, Alzheimer’s. When they give a drug, they have no idea what it does to this processor. And the neocortical column is the elementary processor for human beings to have coherent perception, attention, and memory. This is shocking. I mean, we are living in such a primitive time of medicine, you cannot imagine

 How the Blue Brain will help?

 If you have the model where you’re able to embody all the key parameters, you can start exploring a hypothesis for a disease. When you tweak the model, you can see what kind of pathology occurs. You’ll be able to really isolate very precisely what has gone wrong. If a certain part of the circuit malfunctions, it’s going to display certain symptoms. You can actually simulate and test hypotheses for different diseases. If we know which pathways are malfunctioning, then we can look and see what it means for the circuit, what kind of information is it not able to process. This can guide drug discovery by letting you simulate the effect of a drug on the circuit. You’re going to find out exactly how it operates, what it is altering. Drug discovery is terribly expensive, just to find out how one drug could or could not work and all its side effects. Simulations could cut drug discovery costs by 70 or 80 percent. What we call in-silica-based drug discovery—simulation-based drug discovery—is going to be the future.

A case for Bosco

This newly focus on brain research and computerized reconstructions of the human brain based on biology will require a colossal amount of computer power. It is the natural successor in the big challenges computing has to solve to simulate the brain.

Professor Adan Segev

The leader of Blue Brain Project in Israel is Adan Segev from Hebrew University. He received fundingy from Safra Foundation and as a great achievement we read in the interview:

Since 2001, he has been one of the leaders of the Blue Brain Project, the only participant to have a direct line to the Swiss IBM supercomputer, which costs $20 million and whose cooling alone with Geneva lake water has an annual price tag of $1 million. The supercomputer, he says, takes up about twice the area of his own office

The emphasis is mine: why accessing a super computer is such a privilege and probably only for initiated in this esoteric skill? What Profesor Segev says between the lines is the following

• A single supercomputer, not matter how big, is a limited resource unable to accommodate all researchers in a project of such magnitude
• We need tools to create an infrastructure of hundreds of if not thousands of supercomputing nodes and clusters all over the world
• We need a simple tool to be able to access all these computers from a laptop like Mac

There is a tool, called Bosco . The tool, now in release 1.2 will allow -one day in the near futu student with a Mac connect to clusters and supercomputers.

Project Blue Brain  and the US Brain Activity Map need to provide a democratic access to the resources.

Watch Henry Markram at TED 2012