Donald Doherty's blog

Tag: Brain Science

  • Bio-Commons a Global Challenge

    Science has always been an international endeavor and challenges have always stemmed from this fact including national differences in freedom of travel and speech, national secrecy and competitiveness, and national security to name a few. Changes in information technology and the state of the life sciences in particular are creating new challenges and perhaps heightening old ones.

    The policy forum paper “Research Funding: Sustaining the Data and Bioresource Commons” published today (October 29, 2010) in Science has some welcome viewpoints on these developments although I’m uncertain what they mean by the “globalization of scientific research” since, as stated above, science has always been global.

    Simply stated, the global public needs information repositories that are globally accessible. At one time it was the library at Alexandria. Recently the large repositories have been national libraries like the U.S.A.’s Library of Congress. Most recently the Internet has become a major, if not the main, repository of global knowledge.

    The issue of global access to life sciences data is particularly important right now. The project to understand life, including brain function, is producing vast amounts of data on mechanisms active at multiple scales of time and space.

    We must create a virtual biomedical library for everyone. The data will be too vast for any mortal to read. The library will need to present its data visually and actively. That is, users will need to get into the data intuitively by working with a virtual brain, for instance, and actively investigating its various functions through simulations.

    The way we share knowledge is going through radical shifts in the life sciences. Journal articles as we’ve known them have already changed and will change far more in the future. Humanity is on the cusp of perhaps its greatest project ever. By meeting the global challenge of a bio-commons we will attain levels of biological knowledge and medical practice far beyond what is currently possible.

  • Blind People Perceive Touch Faster than Those with Sight

    The brain’s visual system and, in particular, its visual cortex is activated in people that are blind since early in life. Studies have shown that blind people are better at detecting things touching their skin close together than are people with sight. People that are blind seem to have a particularly acute sense of touch. Are they faster at perceiving touch?

    Dr. Daniel Goldreich’s team just published the paper “Vibrotactile Masking Experiments Reveal Accelerated Somatosensory Processing in Congenitally Blind Braille Readers” (October 27, 2010 in The Journal of Neuroscience) that suggests the answer is yes.

    Fast Braille readers encounter a raised dot about every 50 millisecond. Sighted people would not be able to perceive a raised dot encountered so rapidly. They’d either simply not perceive the first or second raised dot they encountered or they would perceive the two dots as one dot. These phenomena are known as perceptual interference.

    The research team set up a series of experiments to test blind and sighted people on detection and discrimination tasks. They showed that all of their sighted and blind participants performed equally well on simple detection and discrimination tasks. However, on the tasks that included perceptual interference, people blind since early in life differed significantly from those with sight.

    In fact, those blind since early in life were the fastest Braille readers and were able to perceive individual touch stimuli faster than any other group. They concluded that early onset blindness leads to accelerated perceptual processing, which in turn enables rapid Braille reading.

  • Whole Brain Catalog: Brain Cells and Molecules

    Yesterdays post “Whole Brain Catalog: the Google Earth for the Brain” introduced the Whole Brain Catalog. Within the overall framework of a mouse brain hangs a lot of data. Today we’ll look at some of the data you may explore in the Whole Brain Catalog.

    Note: Please read yesterday’s post if you haven’t installed the Whole Brain Catalog on your computer.

    Brain cell data from actual microscope measurements are displayed in the Whole Brain Catalog.

    Let’s start by looking at brain cells (neurons). Data associated with cells of all types are listed under “Cells” in the Data Type area.

    Go to the Data Type area to the left-bottom of the brain viewing area and click on the arrow to the left of “Cells.” This will open the list of cell types and groups of cells available to you. Find the “Mainen-Sejnowski Pyramidal” cell and check the box to the left of the label. Give Whole Brain Catalog a bit of time to download the data.

    Tip: Keep an eye on the status bar at the bottom of the Whole Brain Catalog window. It’s busy if it says “Creating Objects.”

    Once the data are loaded, double-click “Mainen-Sejnowski Pyramidal” in the Data Type area and Whole Brain Catalog will zoom through the brain and show you the pyramidal cell. The yellow wire box surrounds the neuron. To move around the cell click the “Rotate Camera” button. You’re now at a relatively small scale so when you zoom in and out be sure to press your mouse button down just once and hold (rather than twice and hold).

    Would you like to place the brain back into the context of the whole mouse? Adding the skull helps me to do this. In the Data Type area expand “Mesh Models” and look for “Mouse Skull.” Check the box to the left and, after the data load, double click “Mouse Skull” to zoom out and view the skull.

    Tip: You may also bring up a context menu. In Windows use your right mouse button and on Macintosh computers use the command button with your mouse click.

    The mouse skull is displayed along with the brain in the Whole Brain Catalog.

    Now that we’re back at a high-level view of the mouse and its brain we’ll dive down to the very small molecular level and look at a protein molecule. The Whole Brain Catalog displays three dimensional molecular structure data from the Protein Data Bank.

    Go to the Data Type area and click on the arrow to the right of “Mesh Models.” Use the scroll bar to the right of the Data Type area to scroll down until you see “Potassium channel.” Check the box to the left of “Potassium channel” and give Whole Brain Catalog a bit of time to download the data.

    The potassium channel is displayed in the Whole Brain Catalog.

    Double-click “Potassium channel” in the Data Type area and Whole Brain Catalog will zoom through the brain and show you the potassium channel. The yellow wire box surrounding the potassium channel is very small in this standard view. Select the “Zoom In” button and press your mouse button down and hold to get closer. We’re at such a small scale that this slower zoom seems fast. You may find yourself zooming past the molecule. Quick clicks using both “Zoom In” and “Zoom Out” should get you there. Be sure to admire the structure of this molecule by using the “Rotate Camera” button.

    Other related blog posts:

    Whole Brain Catalog: the Google Earth for the Brain