The Quiet Death of the Allen Brain Atlas?

Launched with much fanfare in 2003 with 100 million dollars in start-up money from Microsoft co-founder, Paul Allen, the Paul Allen Brain Atlas now appears to be on its deathbed and on its way to a quiet death after having blown through most of its money and after being abandoned by many of its prominent supporters. One can only hope that their data (i.e., mouse brain in situs) will remain online and openly accessible to the public for years to come.

What exactly is the Paul Allen Brain Atlas? The people behind the Paul Allen Brain Atlas are doing in situ mRNA hybridizations to determine mRNA gene expression patterns for all 20,000 or so genes in the mouse brain. It's definitely something that needs to get done; in fact, it should have been done years ago. That being said, I have several criticisms. For instance, they do not have any data mining tools available and are behind schedule in their software development (for instance, they were supposed to have a 3D atlas viewer desktop application available months ago). They have thousands of data sets, yet they do not make it easy to explore and browse through the data. Their Flash-based user-interface is bloated (and I love Flash in general). Their terms stipulate that you cannot use any of their data for any reason without getting special permissions from them. So, while I think the Allen Brain Project is a worthwhile endeavor and something that needs to be done, I think the people managing the project have done a pretty bad job, to say the least.

Who was it that said that Paul Allen had an inverse Midas touch - that everything he touched turned to shit? Oh, yeah, it was this guy. He may have a point there!

What I'd like to know is whether and how this project can be salvaged. Replacing the management team is one obvious option since these people do not know how to manage this type of project and the diverse skill sets and coordination involved. Another one is learning to be more thrifty with money. You can do a lot of things with a little money. What the Paul Allen Brain Atlas has amply demonstrated is that you can do little with lots of money. Lesson to be learned: too much money can be a hindrance to effective, agile, and rapid project development.

Blue Brain Project Scepticism

The Blue Brain Project is an overly ambitious project aiming to simulate real brains. Two models are planned to be built, one a molecular model of the neurons involved. The other will clone the behavioural model of columns thousands of times to produce a complete neocortex, and eventually the rest of the brain.

The end product is expected to take at least a decade to achieve.

Henry Markram, one of the leading proponents of the Blue Brain Project, had this to say in Feb 2006:

"Alan Turing (1912–1954) started off by wanting to 'build the brain' and ended up with a computer.... As calculation speeds approach and go beyond the petaFLOPS range, it is becoming feasible to make the next series of quantum leaps to simulating networks of neurons, brain regions and, eventually, the whole brain. Turing may, after all, have provided the means by which to build the brain."

Alan Turing notwithstanding, I don't see how the Blue Brain Project can succeed given our current lack of neuroanatomical knowledge, which includes our ignorance of whole-brain neural connectivity. It would seem that we first need to establish a firm neuroanatomical grounding before embarking on any massive modeling attempt that claims to be neurobiologically-plausible. Until that neuroanatomical foundation is established, it is justifiable to remain sceptical about the success of the Blue Brain Project.

What I find amusing, which is evident when you visit the Blue Brain Project site, is that the project places great importance on the neocortical column (NCC), as if this were the magical unit of the brain that explains its function. They disregard the fact that the NCC is interconnected with dozens of other brain areas, including thalamus and midbrain, and is part of a very complicated network. Yet they choose to focus on the NCC as if that were the holy grail of the brain. It's not.

Markram goes on to state:

"Nevertheless, this defeat of a human master (Gary Kasparov) by a computer (Deep Blue) on such a complex cognitive task (chess, which is not so much complex as it is combinatorial) posed the question of whether the relevant world of an organism could simply be described by enough if–then conditions. It could perhaps be argued that artificial intelligence, robotics and even the most advanced computational neuroscience approaches that have been used to model brain function are merely if–then-like conditions in various forms."

In other words, Markram would like to reduce the operations of the brain to a series of if-then-else conditions. This is fine for digital logic and computers, but is inappropriate for analog computing and the inherent nonlinear dynamics of the brain. A few circuit diagrams of canonical circuits of the brain is a far cry from realistic modeling of the intricate complexities of the brain. In my opinion, the Blue Brain Project is doomed to failure. Deep Blue may have beaten Kasparov at the utterly mindless task of combinatorial chess play, but the Blue Brain Project will never, within the foreseeable future, rival a real mammalian brain in function. I would like to be proven wrong on this one, but being intimately acquianted with both the power of simulation and the intricate complexity of the brain, I know I'm not. We are not in a position today to make realistic simulations of the brain. Maybe in a decade or so, we will be.

Note that I am not alone in my opinion:
"This is an ambitious project that is bound to fail. We are still far from understanding enough about the brain to build detailed models"
--Terrence Sejnowski

While I'm very sceptical of the Blue Brain Project, I will be keeping an eye on their progress.

Whither to Neuroinformatics?

“We are alarmed that the NIH
has chosen to poorly support
neuroinformatics under
the NIH Roadmap and Neuroscience
Blueprint initiatives.”
—Gazzaniga et al, Jan 2006.

Is this a sign that neuroinformatics funding is in trouble? If so, what can be done about it?

Granted, the "Decade of the Brain" (1990-2000) was not exactly a stunning success. Just compare it alongside the Human Genome Project's online and offline success to see how far behind neuroscience fell. But this does not necessarily justify the cutback in funding. There are excellent initiatives that have recently emerged. What we need to do is redirect the funding to those initiatives that have a high probability for success, and that have already evinced success. Those initiatives do exist: For example, fMRIdc.org and BrainMaps.org, to name a couple.

Collaborative Digital Brain Mapping Comes of Age

Google Maps and related geomapping services provide high-resolution satellite maps to anyone with an internet connection and have set the standard for online digital mapping. We are now beginning to witness similar digital mapping technologies spilling over into other non-related fields, one of the more interesting of which is neuroscience and the collaborative digital mapping of the brain.

Launched less than a year ago, BrainMaps.org has rapidly developed to lead the field in digital brain mapping technologies. With several terabytes of ultra high-resolution brain image data, consisting of several dozen mouse, monkey, and human brains, its online brain image database is the largest and most diverse currently available. This massive image data is integrated with structural information regarding spatial locations of different brain areas and markers, and the relations between them. And in the collaborative spirit, online users are free to add their own labels and annotations, and to place landmarks throughout the digital brains they explore. Users may even share their images, landmarks, and other annotations with other users in the BrainMaps forum, which in many ways parallels the Google Maps Community, but on a smaller scale.

The U.S.-sponsored 'Decade of the Brain' has come and gone; it officially ended in the year 2000. It would take another five years before BrainMaps.org came onto the scene, and in a way, it encapulates what the Decade of the Brain should have been about: Collaborative digital brain mapping and a resource available to everyone with an internet connection.

The Decade of Reverse Engineering the Brain (2005 - 2015)

We are witnessing a renaissance in brain science and technology. Science is examining the brain in ever increasing detail to discern important components of brain structure and function, all of it leading to a reverse engineering of the brain. Within the last year alone, websites have appeared devoted to mapping the brain in high detail. One of the most stunning of these is BrainMaps.org, where visitors may explore high resolution images of whole human and primate brains, seeing every neuron and every neuron process in vivid detail. We are now at a unique point in history where the brain is no longer viewed as a 'black box', but now, anyone with an internet connection can view every single detail of brain structure online. We are post-'Decade of the Brain' (1990-2000). We are entering the 'Decade of Reverse Engineering the Brain'.