Paul Allen Brain Atlas Misconceptions

I had noticed last Tuesday a blip on the visitor activity site statistics for this blog, and when I looked into it further, saw that increasing numbers of people were coming to this blog by searching for the Allen Brain Atlas. Apparently, this visitor activity 'blip' corresponded to a publicity campaign launched by the Paul Allen marketing department on that same day to publicize that all the genes in the mouse brain had been mapped.

I have posted some things that were critical of the Allen Brain Project, but not unrightly so. I want to see the project succeed and not merely create illusions and spread disinformation through the media. With this in mind, I would like to correct some the media hype and falsehoods about the Allen Brain Project that have been widely circulated.


Common Allen Brain Atlas Misconceptions

1) The Allen Brain Atlas will contain over 1 PetaByte of data.

False. The orders-of-magnitude calculation was done by multiplying 20,000 genes by a trillion neurons, but this is a gross overestimate. A more realistic computation involves multiplying the number of datasets they have, which is around 20,000, with the average size of each dataset. The average size of each dataset is about 10 slices, times the size per slice. The size per slice is about 10,000 pixels wide, which works out to 100 megapixels per slice. Without image compression, each megapixel is 3 megabytes (one byte for each color channel), which means that each slice is 300 megabytes, uncompressed.

Thus, a more realistic calculation of the size of the Allen Brain Atlas is
(20,000 datasets)*(10 slices per dataset)*(300 megabytes per slice) = 60 TeraBytes.

So, the real size of the Allen Brain Atlas is around 60 TeraBytes, which is a far cry from a PetaByte.


2) Since mice and humans share more than 90 percent of genes, the Allen Brain Atlas has enormous potential for understanding human neurological diseases and disorders.

False. We share over 70% with insects and over 50% with plants, so according to the logic of the Allen Brain Atlas people, dissecting the genetic maps of oranges can help us fight heart diseases and schizophrenia.


3) The Allen Brain Atlas will provide the most detailed map of the most complex organ.

False. http://BrainMaps.org provides the highest resolution whole brain maps, and not just for mice, but for primates and other species. The resolution of BrainMaps.org data is over twice as good as that of the Allen Brain Atlas.


4) The Allen Brain Atlas has already led to several significant new findings about the brain.

False. There are absolutely no peer-reviewed publications over any significant new findings from the Allen Brain Atlas. I do believe that significant findings can be made, but there is nothing published about it in peer-reviewed articles as yet. (Update!: in Jan 2007 they did finally publish one article; unfortunately, it contained nothing new and what they were presenting as "new" was in fact old work that had been published by one of the authors, Lein ES, well before the inception of the Allen Brain Atlas.)


5) The Allen Brain Atlas provides a complete genetic map of the mouse brain.

False. It says nothing about silent DNA or junk DNA, not to mention splice variants. Nor does it say anything about genes involved in development or disease, nor about gene expression variance or genetic interactions. Plus, the fact that a large percentage of their probes failed (which means they don't have data for genes they claim they have data for), and in many cases, the data is either wrong, or it's very poor quality.


6) The Allen Brain Atlas gets more than 12 million "hits" a month.

False. As of Feb 24, 2007, the Allen Brain Atlas ranks in at an abysmal #1,173,023 according to Alexa, which means that they bring in no more than a few hundred visitors per day. In other words, the Allen Brain Atlas is a relatively unpopular site.


7) The Allen Brain Atlas utilized factory-like efficiency.

False. Over a period of just three years, over $42 million was spent on the Allen Brain Atlas, which is outrageous (thankfully, taxpayers were not footing the bill). There were 40-50 people employed for the project, which means that probably $4-5 million per year went directly into their pockets for salary. In all seriousness, had the Allen Brain Atlas utilized factory-like efficiency, then there would have been around 10 people employed and the total cost would have been kept between $3-9 million.


8) The Allen Brain Atlas is "Epoch-Making".

False. The Allen Brain Atlas is one of many projects that aim to better map the brain. As such, trying to present the Allen Brain Atlas as the only large-scale "epoch-making" brain mapping project is ludicrous and reflects the self-centeredness and disengagement from reality of the project managers making such claims. I have posted previously about how many of the original prominent people involved with the project deserted it due to mismanagement, disenchantment, and inner power struggles. The problem is that the ideal that originally guided the project three years ago is being substituted for the reality of what the project actually is today. And what it actually is today, while useful, is not all that unique, and certainly not epoch-making by any stretch of the imagination. The disinformation being pumped into the media is something that should raise concerns; my own personal thoughts are that this media disinformation campaign is the result of a lot of money being thrown around. Maybe that's where a lot of the $42 million went that should have been going towards the project, quality control, and better user interfaces.