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.
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.
Labels: allen brain atlas, brain atlas, gene expression
posted by neubrain at 9:12 AM
10 Comments:
it's good to hear someone tell it how it is and not just regurgitate the deceptions and hyperbole of the popular media. Keep up the good work!
it's good to hear someone tell it how it is and not just regurgitate media propaganda. Keep up the excellent work!
That first post my mine too. My bad.
thanks for the positive feedback, John, I mean Pete!
> 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.
Well actually I think we could learn a lot from the genetic maps of oranges. Despite their lack of hearts and brains, I bet that much of what is learned would end up aiding the search for treatments for heart disease and schizophrenia pretty quickly.
Bayle, regardless of whether I agree with what you say (and I don't), it should be noted that the gene expression maps from the Allen Brain Atlas are for a 'normal' mouse brain, which means it says nothing about deviations from normality, including neurological disorders like schizophrenia. Hence, their claim that determining gene expression maps from 'normal' mouse brains will help us understand neurological disorders like schizophrenia is false.
I'm usually doing contra-hoopla, but you seem to have that role covered, so I'm going to run what I think is some mild defense. First, every university and every public research project has PR people who often hyperventilate and otherwise get things wrong in promoting the work of the researchers. I haven't followed the news coverage or PR of the atlas, but I'd be surprised if it were in a different league from what went with the public genome project (plus arguably we could expect news consumers to have been made a little savvier by that onslaught). Secondly, I think you might be judging some of these news claims unfairly, by applying the same language standards with which you evaluate a claim in research report. At least one Allen claim you offer in paraphrase and object to--"The Allen Brain Atlas provides a complete genetic map of the mouse brain"--strikes me as reasonable, depending on the exact context. In particular, the literal claim is not inaccurate. It's linguistically indeterminate. How many biologists will understand "genetic map" in this context as intended to convey what it does in genetics? Approximately zero. So this claim is figurative. Expressly it does claim comprehensiveness relating to mouse brain genes, and to me a map approximating the location and density of all mRNAs at one time point in a mature healthy rat brain satisfies that claim. A map of the United States is "comprehensive" without showing every house and footpath and telling us about everybody's day back to Gondwanaland. I don't think we know, and I'm sure there's no consensus on what "all genes" would mean, and a consensus does exist to go on using the word "gene," in which case characterizing such a set of mRNAs as all genes seems reasonable and even fairly clear. Finally, while I think your paraphrases are great for identifying and clarifying where the public might be confused, I think at least some are inadequate for hanging anybody out to dry, be they PR person, journalist, researcher or Paul Allen. You need quotes and context for that, including the forum or publication in which the words appeared. Tape record the way you talk about your own data when chatting with scientific chums over lunch, while speaking from a podium at a national meeting, and while explaining your work to relatives at Thanksgiving--then compare it to your published papers. Presumably you didn't think you were lying any in any of these circumstances. You're just assessing the meaning of your words as distinct to each context--or conforming to a different vernacular in each. Likewise, "Time" is not "Cell."
thanks Murky Thoughts. Their PR people did get it wrong, and I'm simply pointing that out to correct blatant misconceptions. I'm not trying to poopoo what they've done, only to correct the hyperbole and embrace realism (as opposed to fantasy).
Labatt Brain Tumour Research Centre is holding their Academic Lecture at the MaRS Centre in Toronto on February 7th.
The topic is "What Mouse Models Can Teach Us About Human Brain Tumors"
The speaker, Dr. David H. Gutmann, MD, Ph.D. and Professor, Department of Neurology at the Washington University School of Medicine, does research in mice, trying to develop robust mouse models of human nervous system cancers suitable for preclinical cancer therapeutic studies.
Do the problems with mapping the mouse brain (and applying learnings to the human brain) also apply to mouse brain tumours? I wonder if he would address these points.
http://www.sickkids.ca/BTRC/section.asp?s=Annual+Lectureship&sID=5611
>> bayle said
>> Well actually I
>> think we could learn a lot
>> from the genetic maps of
>> oranges. Despite their lack
>> of hearts and brains, I bet
>> that much of what is
>> learned would end up aiding
>> the search for treatments
>> for heart disease and
>> schizophrenia pretty
>> quickly.
> neubrain said
> Bayle,
> regardless of whether I
> agree with what you say (and
> I don't), it should be noted
> that the gene expression
> maps from the Allen Brain
> Atlas are for a 'normal'
> mouse brain, which means it
> says nothing about
> deviations from normality,
> including neurological
> disorders like
> schizophrenia. Hence, their
> claim that determining gene
> expression maps from
> 'normal' mouse brains will
> help us understand
> neurological disorders like
> schizophrenia is false.
What I meant was only the standard argument that gene expression maps are basic research, and basic research will help everything in biology, including pathological research. This is why I say that even a gene expression map of an orange would be helpful.
I'm sure other people have presented lots of real examples for this sort of thing, but I'll make one up. Let's say that someone else found a gene which was differentially expressed in schizophrenic patients. Now, assuming that gene has a functional homolog in mice, by using the ABA, you could see where that gene is expressed. Using the ABA along with other genetic databases, you can find which other genes co-vary with the target gene. And then using the ABA, you can find where those genes are expressed. And those results might be useful for solving schizophrenia.
Post a Comment
<< Home