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.

Why is Everyone Leaving the Paul Allen Brain Project? Answer: Paul Allen's Sister, Jody Patton

I have been able to confirm the reason why so many people are leaving the Paul Allen Brain Project in droves. Apparently, Paul Allen's sister, Jody Patton, who manages the Paul Allen Brain Project, is an "arrogant", "overbearing", and "incompetent" "dictator" who micro-manages in excess, and whose winning personality poisoned the work atmosphere and smothered creativity, motivation, and initiative. Patton says her management style is "tough but fair", but I say, face reality, Jody Patton got the top management position because her brother is the billonaire Paul Allen, not because she was qualified. Evidently, she is not qualified to manage a project of this size and complexity. The proof is in the pudding; If Jody Patton could manage a project properly, then why is everyone bailing out of the Paul Allen Brain Project? She took a noble initiative to map gene expression throughout the brain and suffocated the life out of it by her incompetence.

So it would appear that my Paul Allen Brain Project Hypothesis is probably wrong, that there is no-one intentionally trying to sabotage the project, but that the Paul Allen Brain Project fiasco was due to Jody Patton's incompetence as a project manager.

Well one good thing to come out of this is that now I know to steer clear of this walking disaster. Paul Allen made a commendable step to advance neuroscience by mapping gene expression throughout the brain, but his big mistake was in handing over the project to his incompetent sister. It is unfortunate that Paul Allen did not possess the objectivity to see the mismatch between his sister and the Allen Brain Project, but then again, Paul Allen's biography reads like a story of failure after failure, and the Allen Brain Project is just another failure to add to the huge list of his. When is he ever going to learn? The Allen Brain Project could have been a blazing success if he didn't appoint his sister to lead the project. If he was more involved with the project, he would have been aware of the problems involved with having her manage and would be in a position to replace her. If Jody Patton had been replaced early on in the Allen Brain Project, when it became evident that she was incompetent, then I have no doubts that the Allen Brain Project would be very successful today. Instead, we have mostly everyone who once supported the project has abandoned it, due largely to Jody Patton's incompetence. It's high time she took responsibility for the projects short-comings. By making this post about it, I am assured that many out there who are interested in what's going on in neuroscience will know the truth.

It has been said that Paul Allen is the accidental zillionaire. Many cried foul at this characterization of him, but after his many mishaps and mistakes, and now the Paul Allen Brain Atlas fiasco which will set back big time neuroscience for at least a decade, I am beginning to think that a better characterization of him would be "the Idiot" (which, as it happens, in his town of Seattle, he actually is known by the name, the "village idiot").

Am I being too hard on Paul Allen and his incredibly incompetent sister, Jody Patton? Nah, I don't think so!