Here are the facts as I understand them from the organizations and individuals involved, as well as media reports. (The quantities of the brains vary slightly, depending on the source.)
On May 31, the assistant director at McLean Hospital’s Harvard Brain Tissue Resource Center (HBTRC) discovered 150 thawed, decayed brains in one of the center’s freezers. Fifty-four of the brains were from children and young adults with autism.
The freezer has two separate alarm systems. One goes off when the temperature drops. The other alarm “calls” five staff members on their cell phones, one after another.
The freezer room is locked.
There are two keys to the room.
There is a surveillance camera in the room.
The freezer is checked twice a day to ensure that the temperature stays at approximately −80 degrees Celsius. The temperature on May 31 was 7 degrees.
In April, all the brain samples, which were normally distributed among several freezers in case of an equipment malfunction, were moved to one freezer in preparation for a visit from Autism Speaks Autism Tissue Program (ATP) staff. Upon completion of the research, the samples were supposed to be redistributed among the other freezers. However, the staff at the center became busy with other work and didn’t have time to do this.
The brain tissue that was in the preservative is okay.
The DNA (which makes up genes) in the defrosted brains is probably okay, meaning those brains may still be adequate for gene research. However, the RNA and protein (which can be altered by environmental factors) is heavily damaged and probably unusable.
The freezer system has never failed in the center’s 35-year history.
The brain samples are owned by Autism Speaks.
OPINIONS AND CONCLUSIONS
Here are several opinions and conclusions for your consideration.
Carlos Pardo-Villamizar, MD, neuropathologist and neurology associate professor, Johns Hopkins University:
The damage to the brains could slow back research a decade. The collection “yields very, very important information that allows us to have a better understanding of what autism is, as well as the contribution of environmental and immune factors.” (In 2004, his study of the autism brains stored in the center was the first study to discover that the immune system is involved in autism.) 
Toni Clarke, journalist, Reuters:
“Freezer failures are not uncommon in research, but for a freezer and two alarm systems to fail simultaneously is perplexing.” 
Geraldine Dawson, Chief Science Officer, Autism Speaks:
Autism Speaks is “in the process of conducting its own independent assessment of the situation.” She wants “to ensure that this unfortunate and rare incident will not negatively affect donations in the future. We remain committed as ever to conducting research that will uncover the causes of autism and allow us to develop more effective treatments. Brain tissue research is crucial to achieving those goals.” 
Stephen Scherer, director, McLaughlin Center for Molecular Medicine, University of Toronto:
“… the incident should be a call to action for other storage facilities and the federal government to pay more attention to freezer safety for the sake of science and donor families. The donors, they should be upset, they should realize that this shouldn’t happen, but this shouldn’t dissuade people from continuing to donate, because it is the most important resource that autism science has right now. If this was to push people from donating going forward, that’s the only thing that would [make this] a worse disaster.” 
Jonathan, Autism’s Gadfly post:
“One wonders who would have motive for tampering with autistic postmortem brains.” … “I wonder what the probability is that right at the time the brains were moved, the alarm system would not happen to work and the thermometer would malfunction. There was a security camera and checkpoints to protect the brain samples. However, this does not rule out an inside job.” 
Emily Singer, M.S., news editor, Simons Foundation Autism Research Initiative:
“The freezer failure is under investigation by both Harvard and Autism Speaks, but so far appears to be the result of an unfortunate series of events.” 
Dr. Francine Benes, director, HBTRC:
“This was a priceless collection.” She goes on to say that “the situation is so unusual—the perfect storm of alarm and thermostat failure and the concentration of samples—that she cannot rule out foul play.” The hospital plans to upgrade security and conduct an internal investigation. 
Peter Paskevich, director of research administration, McLean Hospital
“Every one of our freezers has emergency power in case the electricity fails, and we have CO2 [carbon dioxide] tanks in each freezer to keep the space cool for about 24 hours if the refrigeration fails. … Would you think that everything would fail at once?” 
Teresa Conrick, contributing editor, Age of Autism
“Has the truth about autism and specific damage to brains showing immune system injury become so horrific that some would tamper with evidence?” 
Who’s looking into the freezer failure? So far, HBTRC.
And Autism Speaks. An organization with a Pfizer scientist serving as vice president of translational research and an executive vice president who is a former McNeil Pharmaceuticals employee. An organization that, in 2008, paid more than $17 million in “salaries, other compensation, and employee benefits.”  (See Jeffry’s article from last June entitled “83 Reasons to Question Autism Speaks for Hiring Big Pharma Scientist” for more information.)
I’m surprised that Dr. Paul Offit hasn’t been asked to investigate.
This situation calls for an outside, independent investigation by a completely unbiased group. Anything less is unacceptable. And I’m not talking about someone who is involved in any way with HBTRC. And certainly not someone who’s in bed with Big Pharma.
The freezer failure raises a lot of questions. Here are several.
What is the chance of the freezer failing?
What is the chance of one alarm system failing?
What is the chance of two alarm systems failing?
What is the chance of the freezer AND two alarm systems failing?
Is it a coincidence that the freezer that failed is the one containing the autism brains that had been moved for Autism Speaks ATP staff?
Is it a coincidence that the halves of the brains in the freezer—the ones that were destroyed—are the halves that could point to environmental causes of autism (such as vaccines)?
Can all the factors that contributed to this disaster be a coincidence?
What will an investigation by HBTRC prove? How credible could it be? Even if the center says the surveillance camera shows no evidence of foul play, how could we believe it? How would we know that the camera wasn’t tampered with?
What will an investigation by Autism Speaks prove? (No further questions necessary.)
How can a reasonable person not suspect foul play and question this “unfortunate series of events?”
Will the public—and, even more tragically, the families who donated their children’s brains to research—ever know the truth?