Gut Bacteria-Autism Link May Just Be Misinterpreted Data From a Confusing GUI

Remember that mouse study which concluded gut bacteria may contribute to autism symptoms?

Jon Brock, a cognitive scientist with 18 years research experience on neurodevelopmental conditions, including autism, has posted a Medium post summarizing new critiques of the research emerging online. (For example, from Professor Thomas Lumley, a statistical researcher who has concluded that the study’s analysis “is wrong,” and “arguably due in part to a poor GUI design.”)
Soon after publication, scientists began expressing concerns about the paper on social media. These were echoed in a blogpost by drug discovery chemist Derek Lowe and then in a series of comments on the PubPeer website. Looking more closely at the data, the results are a whole lot less compelling than the media coverage, the press releases, and even the paper itself suggest…

The differences between mice with autistic and non-autistic donors are subtle if they exist at all. And there are reasons to be skeptical about even these small effects. Mice are not tiny humans with tails. Autism is defined in terms of human behaviour. And so the claim that mice showed “autism-like” behaviour relies on an assumption that the mouse behaviours under investigation are in some sense equivalent to the behaviours that define autism in humans…

But even if we accept the premise that mouse behaviours are directly analogous to behaviours exhibited by autistic humans, the evidence is both weak and inconsistent. It’s fair to say, I think, that the authors have presented the data in its most flattering light… Since posting this critique last week, further developments have cast more doubt on the conclusions of this study. The authors responded to criticisms on PubPeer. In doing so, they released the code for their analyses, which appear to show important discrepancies between how the analyses were described in the paper and how they were actually conducted…. Lumley suspects that the culprit is the confusing interface of the SPSS software the authors used for their analyses. There’s no reason to see this as anything other than an honest mistake. But, as Lumley notes in his post, the episode shows the importance of researchers sharing their analysis code as well as their data.

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