Connectomics, Neuroscience, and Computational Models of the Brain

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When an idea in science is stamped a theory most scientists just shrug. Unlike the public they know that theory or not, an idea can’t be taken as ground truth until it has been thoroughly vetted through extensive and redundant experimentation. In 2012 Dr. Sebastion Seung published a book advocating a theory neither new, old, nor entirely his own. The science of some aspects of his idea is, however, becoming quite acceptable to the neuroscience community. His scientific idea is that, aside from our DNA, it is the uniqueness of the pattern and characteristics of connections between the neurons in our brains that makes us who we are. In all fairness, Dr. Seung is not the first to propose this idea, nor is he the only proponent of what has become known as Connectomics—but he has found ample resistance to the idea that our “connectome” could have a role in establishing identity that rivals the uniqueness of our individual genetic code. Many question that the mere architecture of the connections in a brain could yield the rich functionality that we all enjoy. Another established expert in the field, Dr. Cristof Koch said,”Even though we have known the connectome of the nematode worm for 25 years we are far from reading its mind. We don’t yet understand how its nerve cells work.” As Dr. Koch and others have intimated, the more likely whole theory of the brain is a hybrid one taking into account not only connections but also the chemical-laden soupy milieu that neurons sit in.

Connectomics As A Theory Is Great But Incomplete

Imagine yourself as a competitor in a wrestling match. Pretend that before the match you get to choose between two competitions—one option is to wrestle a thoroughly muscled man twice your size, the second is to wrestle 25 small, but very angry, eight year old children. It is likely that you will be overpowered in either case but it is a useful analogy to help you see the differences between connections of neurons. These connections determine how similar, or coupled, the behavior of two neurons are and they are not all the same strength; Some connections are weak, and others are strong. It would take many more weak connections to achieve a similar response from a neuron as you might expect from a few very strong connections. Connections between cells are called synapses, and synapses are essentially a gap across which neurons send chemicals. The upstream neurons typically do most of the sending, and the downstream neuron pays attention to how much the signaling neurons sends.

It is possible, however, for this process to be interrupted. Foreign chemicals, not usually found at the synapse can block or replace those that belong…the results could be dramatic. The body releases specific chemicals on a regular basis— dopamine, serotonin, glutamate, calcium, and many others that are routinely synthesised in the body and play an important role in the way your neurons function. The role that these extra-neural chemicals play is an example of a crucial non-Connectome feature of your brain which contributes to what makes you who you are. While the connectome forms the primary architectural framework on which these processes are possible, it cannot tell the whole story alone.

How To Measure the Importance of Connectomics?

The concept of experimental control is central to what makes scientific results at all verifiable. If you wanted to determine if lavender oil cures cancer you would need to isolate cancerous cells by controlling for all other potentially cancer killing compounds or mechanisms that might also be nearby…otherwise how could you prove that exposure to the lavender was what did the deed? How do you control for the contribution of connectomics to identity when the connectome is never the only variable that changes from person to person? To put it in other words…how do you know that the differences between my connectome and yours is what makes me walk, talk, and think differently than you? How do we know that factors such as environment, genetics, diet, and habits are also coming into play?

We obviously need some kind of experimental control…where we can observe the changes in behavior in a single connectome when exposed to different environments or perhaps the differences in behavior between two connectomes exposed to the exact same environment. It turns out that the easiest, most practical, and ethical method of doing this is to build what is called a computational model…this is essentially a version of the system in question reproduced via mathematical equivalents inside of a computer. If you are a bit mystified as to how this could be done…take the example of a pitcher throwing a baseball. If you knew the trajectory and initial velocity of the baseball, as well as a few essential details about the ball itself, you could predict the path with near perfect precision. Similarly, if you know a few of the rules by which neurons behave, you can predict their behavior with very high accuracy. When you add to that a model of the behavior of connections between cells you have all of the functional components of a connectome. Simulations of connectomes, real and hypothetical, have the power to yield incredibly valuable insights.

Connectomics, A Piece Of The Puzzle And A Clue For Further Investigation

While it is unlikely that a connectome holds all of the information necessary to reconstruct your cerebral identity, it is undoubtedly a crucial component. But how do we test the idea and gauge just how important it is? Computational models can shed some light into the black box of the brain by building toy versions, simple and complex, to explore how variations of the connectome impacts the behavior of a network of neurons. Combined with models of extracellular features of neural systems, we may be able to learn the balance of influence each structural component of our brains hold over our behavior. Like behavior, connectomics is very difficult to study via reductionist methods…it may very well be the completeness of the brain that makes us so special.

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Clayton S. Bingham is a Biomedical Engineer working at the Center for Neural Engineering at University of Southern California. Under the direction of Drs. Theodore Berger and Dong Song, Clayton builds large-scale computational models of neurological systems. Currently, the emphasis is on the modeling of hippocampal tissue in response to electrical stimulation with the goal of optimizing the placement of stimulating electrodes in regions of the brain that are dysfunctional. These therapies can be used for a broad range of pathologies including Alzheimer’s, various motor disorders, depression, and Epilepsy.

If you would like to hear more about the work done by Clayton, and his colleagues, in the USC Center for Neural Engineering he can be reached at: csbingha-at-usc-dot-edu.

Humanism and Brain Technology: The Borg, The Matrix, and The New Voices In Your Head

You don’t have to have seen the kid-flick Goonies to imagine a gadget-savvy adolescent who’s one mission in their little life is to contraption-ize everything. I am, in fact, guilty of “booby”-trapping my room for fun in order to reenact my favorite MacGyver episodes (safely, of course). I was known to string up cords that crossed my little boy bedroom with mostly unknown but very important functions…maybe one string flipped the light switch off when the doorknob was turned so my mom wouldn’t catch me awake after my bedtime. I distinctly remember another set at a high angle so that I could send my dirty clothes across the room to the hamper when it was time to get into bed. While none of these contraptions were very practicable (or sightly), my mom tolerated them for a few days because she knew it was important to let the little engineer in me experiment with ways to make my life easier or better. I probably won’t surprise you by saying that none of my earliest inventions resulted in a significantly increased quality of life…but the spirit of that invention is more important than any of us are aware; that spirit has come be called Humanism, or more particularly: Transhumanism. Transhumanists mostly go unidentified—those that are, typically self-identify—but most find themselves up to their eyeballs in the world of technology. The express goals of this technology fascination is always the same…make being human better.

In order to improve the human condition, Transhumanists must first understand and explore the opportunities for improvement. The improvements must be objective and measurable; this turns out to be harder than it seems. Consider the merits of the gas-powered car…never before have we been able to zoom to and from our destinations with such speed and ease. However, even after a nearly 100 year love affair with the automobile there are still those who are dissatisfied with the improvement and complain about this or that flaw and seem ready to abandon the technology all-together. Consider next, the complexity of the human body…as we introduce drugs and devices are implanted, there are often unintended consequences. The drug that thins our blood makes us prone to bleeding, the drug that calms inflammation compromises the immune system, and the implanted insulin pump often causes serious infections because the tube that crosses the skin collects and delivers bacteria deep into the tissue. Complex systems abound in the body, chief among them is the human brain. 100 billion neurons make upwards of 1000 trillion connections. The unintended consequences of modifying such a system can be severe. For years we saw seemingly savage interventions in the brain such as lobotomies and ablations (essentially cutting out offending parts of the brain), electroshock therapy, and extreme high-dose pharmaceutical therapies with opiates and cocaine, and other psychoactives like Lithium and even Cannabis. Despite the lack of sophistication, the more primitive therapies have only been retired when something apparently better came along; this indicates that the benefits outweighed the known side-effects. We can talk about the unknown side-effects somewhere else. First, stop for a moment and answer this question of paramount importance: what is it about our bodies that makes us uniquely human? Maybe there is more than one answer but it cannot be denied that our brains are the most unique thing about our species as well as our most powerfully evolved feature. Naturally, it is the most tempting target for Transhumanists and their ability and experience enhancing technologies. We are beginning to see these neurotechnologies in clinical settings as well as in the hands of the private consumer—they arrive in the form of implants, uploads and downloads, assistive intelligences, brain computer interfaces, and many other creative modalities.

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Implants and The Borg

The seemingly stray reference to the evil race of humanoid robots from Star Trek is more apt than you know. The very laboratory that I work in is founded on the goal of implementing a computer chip to replace damaged parts of the brain—particularly the hippocampus (which is responsible for memory management). How much of your brain must you replace with computer componentry before you become Borg? That is a question for the philosophers—the reality is that there are members of our community that are severely hindered by dysfunctional brains and implants are a popular proposed solution to the problem. In fact, there are thousands of these devices already deployed around the world: the Cochlear implant and the Deep Brain Stimulator are very effective at correcting some types of hearing and motor disorders. Other devices correcting more complicated disorders are in the pipeline.

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Uploads, Downloads, and The Matrix

If sticking really big needles into your head or neck creeps you out you can rest assured that there will likely be less invasive or scary ways to “upload” your brain or “download” things to your brain. Types of imaging using really powerful magnets and dyes have been developed that may soon have the resolution to peer into the tightest corners of your brain and extract information such as where neurons are, where they send their branches, who they connect to, and perhaps even how strong that connection is. With this information, it is conceivable that engineers could reconstruct many of the important features of your brain in a computer model…essentially taking a snapshot of what it is that makes you you—voile brain uploaded. The download is both much more complex and much more simple at the same time…information in the brain is encoded in individual neuron “spikes” and can therefore be modulated by inducing these spikes in a pre-programmed manner. By encoding an outside message into this spike-language and inducing this pattern of activity in the right region of the brain you can effectively communicate directly to the brain any piece of information which you can reduce to this spike-language. A lot of work is being done to do exactly this. Retinal implants and Cochlear implants are still the most successful examples of this method of information delivery. They by-pass the eyes and ears and communicate outside visual and auditory stimulus directly to the brain in a way that the brain understands. Other applications such as that in my own lab have more complicated hurdles to jump because we don’t yet understand at an abstract level what the stimulus of other brain systems are. This makes translation into and out of spike-language difficult.

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Assistive Technologies and Brain Computer Interfaces (Jarvis, The Red Queen, and the little voice in your head)

While Siri and “Ok Google” are a far cry from what we hope to finally achieve in artificial intelligence, their application is very Transhumanist! Their primary purpose is to help us navigate the world of information and find the best answers quickly. They also operate as a more high-level interface with the device on which they live. Advances in neurotechnology suggest that it may someday be possible to merge this assistive technology with an implant and use it to directly modulate brain activity…uploading and downloading information to and from our brains constantly. This would allow you to keep a steady finger on the pulse of information most relevant to your moment to moment interests. If you aren’t convinced of the power that this could hold…imagine how test-taking would necessarily require more creativity instead of simply recall, or how about all of those almost acquaintances who’s name you can’t remember…wouldn’t it be nice to have their name and pertinent details whispered to you discreetly in your time of need? All of this and more is imaginable given the current trajectory of neuroscience and technology research.

Humanism is Optimism and Materialism Combined

Lets briefly explore the motivations of someone who wishes to improve the human experience or condition with technology. They obviously don’t envision the end of humanity within their lifetimes, nor do they struggle to see the value of easing some of the challenges humans face. You might say this makes up most of the population…I would agree. Humanism, and Transhumanism by extension, is a nearly-innate philosophical world-view that, in my opinion, one must try very hard to be talked out of. Optimism is at the very core of what makes a Transhumanist tick…they only want to imagine a world better or more awesome and interesting than the one they live in. Their means to bringing that about? Technology…But why not politics, or social activism, or journalism? Let me answer your question like this…can you think of anything in the past decade that has enacted more social change than Facebook, or provided more educational opportunity than Google, or put more power (literally) into the hands of the people than Apple or Samsung? While we may not necessarily prescribe to the world-view of these companies we can immediately see the power for change provided by technological advancement. It opens the eyes of the public to new ideas and ways of living. Transhumanism may be optimism, and it may be materialism, but it is also one of the most truly modern and rational work philosophies.

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Clayton S. Bingham is a Biomedical Engineer working at the Center for Neural Engineering at University of Southern California. Under the direction of Drs. Theodore Berger and Dong Song, Clayton builds large-scale computational models of neurological systems. Currently, the emphasis is on the modeling of hippocampal tissue in response to electrical stimulation with the goal of optimizing the placement of stimulating electrodes in regions of the brain that are dysfunctional. These therapies can be used for a broad range of pathologies including Alzheimer’s, various motor disorders, depression, and Epilepsy.

If you would like to hear more about the work done by Clayton, and his colleagues, in the USC Center for Neural Engineering he can be reached at: csbingha-at-usc-dot-edu.

Your Smart Phone Will Get An IQ Bump From Neuromorphic Chips

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In 2008 I came back from having spent two years abroad. During this time many things happened that contributed greatly the current technology landscape. Facebook became open to the public, Youtube hit its stride, and the iPhone was first released. While it wasn’t the first “smartphone” per se…the iPhone was the first truly popular one. Within two years the market’s appetite for smartphones has grown from non-existent to staggering. By the end of 2015 it is estimated that there will be 2 billion mobile devices in circulation. While this signals tremendous progress for computing, it is fair to wonder what it is about these phones that makes them “smart”. There is no doubt as to the reason they represent a huge advancement in mobile technology—the newest mobile microprocessors are virtually indistinguishable from their desktop counterparts in architecture, and nearly a match for many of the entry-level machines in performance. But does that make them smart? Not yet. We use the word smart to describe a human trait—the ability to learn, which may be synonymous with intelligence. While it wouldn’t be productive to get into the semantics of intelligence, it is clear that, “smart” phones don’t pass the test. But there is a technology in the pipeline that will allow phones to learn, and adapt, in order to provide better solutions to our problems.

The Bridge Between Brains and Computing

Late last year IBM introduced TrueNorth neuromorphic technology and later this year Qualcomm will introduce the Kryo (a similar architecture) into production. These chip is not your typical grid of transistors. In fact, it is designed to mimic your brain. Engineers have found a way to reimplement neural networks by using resistors and capacitors (resistors provide resistance and capacitors are like miniature batteries) in parallel and in series. This hardware, while a recognizable simplification of the biological systems it is modeled after, are capable of learning in a manner reminiscent of the way that our own neurons learn.

The journey to a successful neuromorphic chip has not been a short one. The first artificial neural networks were being tinkered with in the 40’s by Warren McCulloch and Walter Pitts. Even then it was postulated that we might be able to someday build something of an artificial brain and harness its computational power as a sort of personal assistant or perhaps let it loose to work on the biggest problems of the day. While actually achieving this is a long way off and there are many complicated hurdles remaining some of these science fictions have become reality in very important ways. No one has yet managed to build a complete human brain but we have been able to simulate large portions of it with biologically realistic features. When I joined the Center for Neural Engineering (CNE) at University of Southern California in late 2014, researchers there were already using thousands of computers to reconstruct and simulate up to a million neurons in a very biologically realistic computational model of the Hippocampus. We called ourselves the multi-scale modeling group because we incorporated complex details of the brain at multiple scales including: detailed models of synapses, beautiful and morphologically appropriate models of neurons, all arranged and connected according to what we had observed in experimental studies of the Hippocampus. The primary purpose of this work, at the time, was to explore the possibility of replacing dysfunctional portions of the Hippocampus with a computer chip. As of this writing, CNE has successfully tested such a device in rats, macaques, and has just completed preliminary testing in humans. Such a device, which incorporates complex math and analog electrical hardware, is able to function by mimicking the computation that might have been performed by a network of neurons.

Why Your Phone Needs a New Brain

You may have noticed a few interesting new features in Facebook’s photo tagging system in the past couple of years. Of particular interest is the ability of the site to recognize faces. While very impressive, humans outperform all but the very best algorithms with much greater efficiency. How is it that your brain is so much better at this exercise than an algorithm? The answer lies in the architecture of your brain and how it learns. Your brain learns by crafting a network of cells to look for small features of a persons face. Particular facial characteristics cause neural networks to respond with a unique pattern. This pattern is then identified as the facial response pattern of that individual. If trained adequately, this type of facial recognition can happen with electric speed (a bit slower because actual connections between neurons are mostly chemical, not electrical).

In general, pattern recognition problems are prime areas of improvement in computing. Because mobile computers are so often presented with pattern stimulus (route planning, video, images, sound, etc.), they are the prime application for neuromorphic chips and really are the place where they are able to make the biggest impact. Look forward to your phone getting a lot smarter in the near future…it is gonna get a new brain.

Add some meat to your social media feed…follow The Public Brain Journal on Twitter

Clayton S. Bingham is a Biomedical Engineer working at the Center for Neural Engineering at University of Southern California. Under the direction of Drs. Theodore Berger and Dong Song, Clayton builds large-scale computational models of neurological systems. Currently, the emphasis is on the modeling of hippocampal tissue in response to electrical stimulation with the goal of optimizing the placement of stimulating electrodes in regions of the brain that are dysfunctional. These therapies can be used for a broad range of pathologies including Alzheimer’s, various motor disorders, depression, and Epilepsy.

If you would like to hear more about the work done by Clayton, and his colleagues, in the USC Center for Neural Engineering he can be reached at: csbingha-at-usc-dot-edu.