Showing posts with label information space. Show all posts
Showing posts with label information space. Show all posts

Thursday, April 6, 2023

Ancient Computers


Cerebral cortexes are cool and all, but the "dumber" parts of the brain have a lot of good secrets in there too.

Lost fish find their way, thanks to their 'ancient brain'
Dec 2022, phys.org


They put tiny translucent zebrafish, barely half a centimeter in length, in a virtual reality environment that simulates water currents.

The researchers expected to see activation in the forebrain -- where the hippocampus, which contains a "cognitive map" of an animal's environment, is located. To their surprise, they saw activation in several regions of the medulla, where information about the animal's location was being transmitted from a newly identified circuit via a hindbrain structure called the inferior olive to the motor circuits in the cerebellum that enable the fish to move. When these pathways were blocked, the fish was unable to navigate back to its original location.

These findings suggest that areas of the brainstem remember a zebrafish's original location and generate an error signal based on its current and past locations. This information is relayed to the cerebellum, allowing the fish to swim back to its starting point. This research reveals a new function for the inferior olive and the cerebellum, which were known to be involved in actions like reaching and locomotion, but not this type of navigation.

via Howard Hughes Medical Institute: Misha B. Ahrens, A brainstem integrator for self-location memory and positional homeostasis in zebrafish, Cell (2022). DOI: 10.1016/j.cell.2022.11.022

Image credit: Homotopical Topology by Fomenko and Fuchs


Friday, February 10, 2023

Neural Cartography


This first article doesn't sound like the cartography I came here for, but it's in the title so...
Researchers present insight into the neural cartography of smell
Oct 2022, phys.org

Honestly I'm unclear as to what this means; the endoplasmic reticulum has some mediating influence on the neural computations that turn olfactory receptor stimulus into the olfactory perception of a specific odorant?

"It is mind-blowing," said Dr. Lomvardas, also a professor of neuroscience and of biochemistry and molecular biophysics at Columbia's Vagelos College of Physicians and Surgeons. "This system found a way to create a genetically encoded, hard-wired means of transforming randomly-chosen receptor identity to a very precise target in the olfactory bulb."

Perhaps, olfactory neurons are not alone in the way endoplasmic reticulum stress organizes their wiring with downstream neurons. "If it turns out that all neurons do this, this discovery could help us understand much more about the brain," said Shayya.

via Mind, Brain and Behavior Zuckerman Institute at Columbia University:  Hani J. Shayya et al, ER stress transforms random olfactory receptor choice into axon targeting precision, Cell (2022). DOI: 10.1016/j.cell.2022.08.025



Here's another article that makes reference to "maps" but isn't actually about navigation...
Mapping the path from smell to perception
Nov 2022, phys.org

"The last frontier of sensory neuroscience"

Because previous studies of the olfactory cortex failed to find any logical organization among neurons there, many neuroscientists suspected information about odors was relayed randomly through the brain. But those studies examined connectivity patterns of just a few dozen neurons.

DNA-based brain-mapping technologies charting the way sensory information is routed between olfactory-processing parts of the brain including the olfactory bulb, which receives sensory information from the nose, the primary smell-processing hub called the piriform cortex, and several other brain regions that receive inputs from the olfactory bulb.

via Cold Spring Harbor Laboratory: Yushu Chen et al, High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex, Cell (2022). DOI: 10.1016/j.cell.2022.09.038


And finally, a little something about how we use olfaction to navigate...
Flies smell the motion of odors and use it to navigate, study finds
Nov 2022, phys.org

Flies can sense the direction of moving odor packets themselves, not just the wind.

Cool study design: They genetically modified fly antennae to detect light, then created fictive odor packets out of light and watched how the flies responded to these signals in both windless and windy environments.

via QBio Institute at Yale: Nirag Kadakia et al, Odour motion sensing enhances navigation of complex plumes, Nature (2022). DOI: 10.1038/s41586-022-05423-4

Tuesday, June 28, 2022

Navigating the Information Gradient


Olfaction is so primitive in its function, that it's an ideal model for all kinds of things,  including navigation, but even moreso, information processing. The olfactory system might be the most effective information processing system we know of, and it's something we've barely begun to investigate. 

Chemotaxis doesn't make headlines often, but it should, because it's ultimately an information-processing problem (and the last time I checked, we were living in the Information Age).

Image credit: A smellmap of Amsterdam by Kate McLean circa 2017 at sensorymaps.com


Information processing constrains how E. coli bacteria navigate chemical gradients
Jan 2022, phys.org

Information that E. coli bacteria gather from their environment limits their performance at chemotaxis, the process by which they guide their movements in response to chemical signals.

And it's funny that they decided to use chemotaxis to test this, about using information efficiently, so in other words, chemosensation is a good model for testing and understanding how information is processed, biomimetically, if you will.

And why do we care? Because chemotaxis and olfaction are the same, at a primitive level. Not much has changed between the way E. coli navigates its environment and the way we do it.

"We wanted to test a broad biological hypothesis: that organisms make the best use of the information they acquire to perform behaviors and other functions. To investigate this, we needed a behavior simple enough that we could quantify how much information it needed and chemotaxis by the bacterium E. coli is a perfect example of such a behavior."

We realized we could measure the amount of information a bacterium was able to gather (in bits per second), while also understanding how much information they would need to navigate at the speeds observed."

To achieve this, they first set out to calculate the theoretical performance limit, which is the maximum speed at which a bacterium could navigate up a chemical gradient, based on a fixed rate at which it acquires information about chemical signals.

Finding the response strategy that maximized gradient-climbing speed with a fixed information cost resulted in the performance limit.

"We found that while climbing shallow gradients E. coli get very little information from their environment, about 0.01 bits/s.

via Yale: H. H. Mattingly et al, Escherichia coli chemotaxis is information limited, Nature Physics (2021). DOI: 10.1038/s41567-021-01380-3


Understanding how bacteria seek out and move towards food
Feb 2022, phys.org

Chemotaxis is the process of attraction in the direction of a chemical gradient. The primary way that organisms control their motion and progressively move toward a target is by inhibiting tumbling when sensing that the chemical concentration is increasing along their current direction.

The research team used stochastic optimal control theory (instead of linear control theory) to find the best possible fully nonlinear sensing and control strategy of run-and-tumble motion (of E. coli) in environments with noisy chemical gradients.

And it looks like chemotaxis, which is the progenitor of olfaction. It is not a stretch to say that olfaction is a form of chemotaxis, and we move through a room to locate a source by using the pattern of its vaporized chemical essence in the air in the room. We calculate its distribution pattern (by stochastic optimal control theory, apparently^), predict the source, and move towards it, updating as we go. The only difference here is that we use legs, and a pretty complex limbic system, whereas E. coli just tumbles and tumbles in the chemovoid. 

via University of Tokyo Institute of Industrial Science: Kento Nakamura et al, Optimal sensing and control of run-and-tumble chemotaxis, Physical Review Research (2022). DOI: 10.1103/PhysRevResearch.4.013120

Odour-Spatial Map - Diogo Matias - Champalimaud Foundation - 2021 [link]


Neurons in the olfactory cortex link smells to places
Feb 2022, phys.org

Sometimes it's good to have someone else say things like this, for a change: 

The researchers focused on the primary olfactory cortex. "The olfactory system is unique among the senses," said the study's senior author, Zachary Mainen, a principal investigator at the Champalimaud Centre for the Unknown in Portugal. "Only olfaction has direct reciprocal connections to the hippocampal system, which is involved in memory and navigation."

It looks like neurons in the posterior piriform cortex (part of the primary olfactory cortex) are encoding place information just like hippocampal cells, and especially behaviourally significant spots. So it's real -- smells are not just smells, they are places and smells at the same time; we can't extricate them from each other, at least not for some brain cells.  

via Champalimaud Centre for the Unknown: Cindy Poo, Spatial maps in piriform cortex during olfactory navigation, Nature (2021). DOI: 10.1038/s41586-021-04242-3

Post Script:
How the brain navigates cities: We seem to be wired to calculate not the shortest path but the 'pointiest' one
Oct 2021, phys.org

When people navigate through a city, they use not shortest path, but instead, pedestrians appear to choose paths that seem to point most directly toward their destination, even if those routes end up being longer, and this is called vector-based navigation.

via  Massachusetts Institute of Technology: Paolo Santi, Vector-based pedestrian navigation in cities, Nature Computational Science (2021). DOI: 10.1038/s43588-021-00130-y


Thursday, August 25, 2016

Getting At the Collapsed Dimension

aka Disembodied Navigation of High Dimensional Reality

Alex Grey – Sacred Mirrors

Oops. I just dropped a clear thumbtack on a white floor. I used to hate that, until I learned the trick. You have to collapse the dimension.

Without hesitation, I drop to the ground, lowering my plane of vision until I’m sideways, eyesight scooting across the surface of the floor, until – there it is; I found my thumbtack.

From above, the visual information of the tack is similar to that of the floor. There’s no edges to be distinguished. Viewing the floor as a one-dimensional line (once your head is level with the floor) instead of a two-dimensional plane (as seen from above) makes the thumbtack plain-as-day. The thumbtack is then the only thing that penetrates into the second dimension – it is the only thing that raises above the floor.

If what you’re trying to do is disentangle the information of the tack from the information of the floor, then reducing the information of one make the remaining asymmetry obvious. A floor is essentially 2-D, and a tack is 3-D. And by “collapsing” your visual field to 1-D (by now seeing it as a line stretching above and below you, with the floor on one side and everything else on the other), the “leftover dimension” of the tack becomes immediately apparent. This is not so much about science-fiction space-folding dimensionality, but about information in general.

In the highly abstract, “disembodied” discipline of information science, dimensionality is not about space, or what I like to call body space. Body space is the three dimensions we are so familiar with, it is a volume and we are in it. But this is only one way of using dimensionality. (The imaginings of Flatland will only get us so far.) In essence, a dimension is a line of potential measurements. It doesn’t have to be about direction like NSEW. It can be in lightness or darkness, as in the one-dimensional measurement of the rods in our eyes. The spectrum of colors is another one-dimensional measurement used for seeing. Together, these two dimensions can generate a third piece of information which is the point in-between the two (and is the difference between pink and navy blue). This is now a measurement of the two measurements. The very idea of dimensionality is for creating this information space as a way for recognizing and manipulating complex patterns in our environment.

Color uses three dimensions, which are lightness/darkness, red-blue (rainbow spectrum), and brightness/dullness (similar to but not the same as light/dark). So “color” is (according to art academia) a piece of 3-D information; it is a measure of the three measurements. And vision in general is not dependent on color alone, but other things, particularly spatial positioning. But let’s stick to color.

What happens when we compare color to smell? Things get different. Smells only have two dimensions, “good” and “bad”. Then again, and just as valid, smells can have infinite dimensions. Recognizing a smell as “good” or “bad” is the highly subjective alternative, and shows more about culture and the individual than it does the smell itself. There must be another way.

To date, there is no comprehensive, universal organizing principle for odors. Some attempts use a multidimensional odorspace, such as Henning’s prism. Theoretically, any smell can be categorized, or identified, as a point in a prism. The vertices of the prism are Flowery, Foul, Fruity, Spicy, Burnt, and Resinous. Something called “Fruity” will sit right in the corner of the prism. Other odors can be in-between two or more odors, so that “Citrus” might be somewhere between Fruity and Flowery (and just a bit towards Foul?).  This is how odors start to drift away from the vertices, and then the edges, and then from the planes themselves into the middle space of the prism. Again, each point, or odor, is now in-between all the odor-classifying vertices. Technically this is a hybrid model, because there are 6 primaries, but the corresponding odor-points are represented inside a 3-D form. (Please note that the original Henning’s odor prism was meant to deliver information on the edges and between the vertices; the smells were not meant to be read inside the prism but on its surface, making it only a 3- or 4-dimensional odor space.) [By the way, check out this Cabinet article on other ways of organizing scents.]

Hennings Odor Prism

There is another way one can imagine a wheel with 6 spokes, where the points at the end of the spokes are primary odors (popcorn, mint, lemon, etc.).  Every identifiable smell looks like a misshapen, spiderwebbed splat reaching further outwards towards the smells it is similar to, and sinking down to the middle where it isn’t. This is a hybrid also, for the final piece of information is a 2-D shape, based on 6 dimensions.

Let us try one more. Imagine a ball with spikes sticking out in hundreds of directions, each one a primary odor. Any given odor is understood as being “between” these hundreds of primaries, as a measurement of the hundreds of measurements.

Here’s an example of a Radar Chart.


This is the idea of a high dimensional information space. It’s a pretty alien idea to us body-users, but not to the algorithms that run our lives, and apparently not to the nose on our face. Thinking about how we categorize smells is perhaps a step in the direction of making ourselves more at home in high-d reality.