After providing all the funding for The Brain from Top to Bottom for over 10 years, the CIHR Institute of Neurosciences, Mental Health and Addiction informed us that because of budget cuts, they were going to be forced to stop sponsoring us as of March 31st, 2013.

We have approached a number of organizations, all of which have recognized the value of our work. But we have not managed to find the funding we need. We must therefore ask our readers for donations so that we can continue updating and adding new content to The Brain from Top to Bottom web site and blog.

Please, rest assured that we are doing our utmost to continue our mission of providing the general public with the best possible information about the brain and neuroscience in the original spirit of the Internet: the desire to share information free of charge and with no adverstising.

Whether your support is moral, financial, or both, thank you from the bottom of our hearts!

Bruno Dubuc, Patrick Robert, Denis Paquet, and Al Daigen




Friday, 13 November 2020
Serious problems in the reproducibility of brain imaging results

As I’ve pointed out in previous posts, the results produced by brain-imaging technologies such as fMRI are subject to at least two limitations. First. they detect neural activation only indirectly, by monitoring blood flows in the brain. Second, the methods used to analyze such images are subject to many forms of bias. These limitations were confirmed in a troubling study by Tom Schonberg, Thomas Nichols and Russell Poldrack, entitled “Variability in the analysis of a single neuroimaging data set by many teams ”, published in the May 20, 2020 issue of the journal Nature.

This important study was summarized in another article, in the journal The Scientist. As this article describes, Schonberg and his colleagues asked 70 independent research teams to analyze the same set of data collected in an experiment using fMRI. In the end, the study found, no two teams chose the same approach to analyze these data, and their conclusions were highly variable.

The study’s authors had no difficulty in recruiting 70 research teams to participate. The field of brain imaging, like the field of psychology, has for many years been facing a crisis regarding the reproducibility of its findings. As is well known, being able to obtain the same results when another term of researchers applies the same protocol is a basic principle of the scientific method. But the topics examined in psychological studies and brain-imaging studies are becoming more and more complex, so that the data are becoming less and less clear. Hence researchers must apply all sorts of methods to, for example, increase the clarity of the signal relative to the background noise or to correct errors due to head movements by the subjects of brain scans. Also, they must calculate statistics that apply the concept of a threshold above which the results may be regarded as statistically significant. A huge variety of statistical methods are available, and for various reasons, most of the 70 research teams did not choose the same one.

As the authors of the study themselves admit, all of this led to results that were fairly discouraging in terms of uniformity. And yet the task that the 108 subjects were asked to perform in the original study that produced the data was fairly simple. While undergoing an fMRI scan, they had to decide whether or not to bet a certain amount of money. The 70 research teams were supposed to test nine hypotheses about the increase or decrease in neural activity that occurred in various parts of the brain when the subjects made their decisions. On some of these hypotheses, there was broad consensus. For example, the hypothesis that activity in the ventromedial prefrontal cortex would decrease when the subjects lost money was confirmed by 84% of the teams, and three other hypotheses were rejected by over 90% of them.

But for the five other hypotheses, the team’s conclusions showed a great deal of variability. This variability confirmed what many researchers in this field had feared: there were simply too many degrees of freedom in the choice of analytical methods available to them. And to correct this huge problem, the scientific community will have to make several changes. First, for full transparency, researchers will have to provide the smallest details of the choices made in their data analyses. Researchers should also be required to record their hypotheses in advance, so that they cannot adjust them subsequently to fit the data (a practice known as sharking). Lastly, researchers should always try to analyze their data with multiple methods of statistical analysis and a variety of parameters. Such constraints may be burdensome, but they are the only way to prevent the current anomalies and will make it easier to separate real, robust effects in brain-imaging experiments from effects that are mere artifacts of the analytical methods chosen.

From the Simple to the Complex, From Thought to Language | Comments Closed


Tuesday, 13 October 2020
Our perceptions are shaped by the possibility of imminent actions

Affordances are a key concept in cognitive science, first advanced by J.J. Gibson in 1966. As I explained in an earlier post in this blog, an affordance is an opportunity that an object offers to take action. A hammer, for example, offers the opportunity to be grasped by its handle, and a chair offers the opportunity to sit down. What is interesting about this concept of affordances is that the opportunity for action does not depend on an object’s characteristics in any absolute sense, but instead is relative: it depends on the possible relationships that a particular organism may establish with that object. A tree, for example, offers different affordances to humans, who may use it as shelter from the rain, or crows, which may use it as a perch, or to woodpeckers, which may use it as a place to hunt for food. Moreover, as the above illustration suggests, any given object (again, such as a tree), may inspire different affordances for a given organism (such as a human) depending on that organism’s motivations and/or the broader general situation. (more…)

Body Movement and the Brain | Comments Closed


Wednesday, 30 September 2020
The expertise account, or, why the brain’s face-recognition area can be activated by the sight of a chessboard

In a 2017 article on the chess website chessable, entitledBeating Magnus after a month of training: the neuroscience of why learning chess is so much harder than learning a language”, author David Karmaley writes: “A fascinating finding from neuroscience is that your brain starts using the fusiform face area to store chess positions! This is the part of the brain usually responsible for human face recognition.”

Karmaley seems surprised that a part of the brain associated with face recognition is also used to recognize the positions of pieces on a chessboard, and at first glance, the connection may seem puzzling. But a theory known as the expertise account offers a highly plausible explanation. (more…)

From the Simple to the Complex, From Thought to Language | Comments Closed


Wednesday, 9 September 2020
The combined effects of meditation and magic mushrooms

Today I want to tell you about a study entitled “Psilocybin-assisted mindfulness training modulates self-consciousness and brain default mode network connectivity with lasting effects,” which a research team from the University of Zurich published in the journal NeuroImage in August 2019. As the title suggests, this study combined two methods of modulating the brain: engaging inmindfulness meditation and taking the hallucinogen psilocybin, a psychoactive molecule found in “magic mushrooms”. Previous studies had shown that both of these methods produced a similar effect: they gave subjects the impression that the boundaries between their bodies and their environments were dissolving (a state of consciousness often referred to as ego dissolution). But in this study, the research team wanted to find out whether combining these two methods might make this effect stronger and longer-lasting. (more…)

The Emergence of Consciousness | Comments Closed


Tuesday, 18 August 2020
How labelling brain parts functionally can be overly simplistic: the cerebellum as a case in point

Today I’d like to talk about the cerebellum. To introduce this topic, I’ll remind you that as animals’ bodies evolved and became more complex, they were subjected to greater adaptive pressures to move more and more efficiently, and the cerebellum is a brain structure that was closely involved in this process.

Here’s the most surprising fact about the cerebellum. The human brain as a whole contains about 86 billion neurons. The cerebral cortex accounts contains about 16 billion of these neurons and accounts for about 80% of the brain’s weight. In contrast, the cerebellum accounts for only about 10% of the brain’s weight, but contains nearly 69 billion neurons! Thus more than three-quarters of the neurons in the human brain are located in the cerebellum, even though it is a small structure compared with the brain as a whole. (more…)

Body Movement and the Brain | Comments Closed