first rough draft of evolution of neocortex and the ring of fire!

Author: rcoreilly

citedrefs.json

@@ -3,7 +3,7 @@ Categories = ["Activation", "Learning", "Neuroscience"]
 bibfile = "ccnlab.json"
 +++
 
-The **neocortex** ("new cortex") or **cerebral cortex** (often just referred to as "cortex") is the [[evolution|evolutionarily]] most recent, outer portion of the brain (i.e., the _telencephalon_, also know as the _pallium_ in other vertibrates) where most of advanced cognitive functions take place. This [[anatomy|brain area]] is the primary focus of the [[Axon]] framework, both in terms of activity dynamics and learning mechanisms. It is unique in having extensive [[bidirectional connectivity]] among excitatory neurons (also known as _recurrent connectivity_), whereas most other brain areas only have such connections involving inhibitory neurons.
+The **neocortex** ("new cortex") or **cerebral cortex** (often just referred to as "cortex") is the [[evolution|evolutionarily]] most recent, outer portion of the brain (i.e., the _telencephalon_, also known as the _pallium_ in other vertibrates) where most of advanced cognitive functions take place. This [[anatomy|brain area]] is the primary focus of the [[Axon]] framework, both in terms of activity dynamics and learning mechanisms. It is unique in having extensive [[bidirectional connectivity]] among excitatory neurons (also known as _recurrent connectivity_), whereas most other brain areas only have such connections involving inhibitory neurons.
 
 The connectivity of the neocortex is organized into multiple different specialized areas of processing, and each such area has a similar laminar structure with 6 distinct layers of neurons. These multiple areas correspond to the "deep" layered organization of [[abstract neural network]]s, which demonstrably provide important computational power. At a cognitive level, this power arises from the process of [[categorization]], where multiple stages of [[neuron detector]]s progressively develop more abstract, general, and powerful ways of representing the world, which then support more systematic and appropriate behaviors even in novel environments.
 
@@ -25,7 +25,7 @@ The inhibitory neurons can be understood as "cooling off" the excitatory heat ge
 {id="figure_lamina" style="height:30em"}
 ![A slice of the visual cortex of a cat, showing the six major cortical layers (I - VI), with sublayers of layer IV that are only present in visual cortex. The first layer (I) is primarily axons ("white matter"). Reproduced from Sejnowski and Churchland (1989).](media/fig_cortex_bio_layers.jpg)
 
-The neocortex has a characteristic 6-layer structure ([[#figure_lamina]]), which is present throughout all areas of cortex ([[#figure_arealayers]]). However, the different cortical areas, which have different functions, have different thicknesses of each of the 6 layers, which provides an important clue to the function of these layers, as summarized in [[#figure_layers-in-hid-out]]. The anatomical patterns of connectivity in the cortex are also an important source of information giving rise to the following functional picture:
+The most evolutionarily recent areas of neocortex have a characteristic 6-layer structure ([[#figure_lamina]]), which evolved from a simpler form of _mesocortex_ (also known as _archicortex_ or protocortex_), as discussed in [[evolution#Evolution of neocortex]]. This laminar structure varies across different areas of cortex ([[#figure_arealayers]]), in ways that are consistent with the different functions of these areas, as summarized in [[#figure_layers-in-hid-out]]. The anatomical patterns of connectivity in the cortex are also an important source of information giving rise to the following functional picture:
 
 {id="figure_arealayers"  style="height:30em"}
 ![The thickness of the different cortical layers varies depending on the location in cortex --- this is an important clue to the function of these layers (and the cortical areas). A) shows primary visual cortex (same as the previous figure) which emphasizes input layer 4. B) shows extrastriate cortex which processes visual information, and emphasizes superficial layers 2,3. C) shows primary motor cortex, which emphasizes deep layers 5,6. D) shows prefrontal cortex ("executive function") which has an even blend of all layers. Reproduced from Shepherd (1990).](media/fig_cortex_bio_arealayers.png)
@@ -34,7 +34,7 @@ The neocortex has a characteristic 6-layer structure ([[#figure_lamina]]), which
 
 * **Hidden** areas of the cortex are so-called because they don't directly receive sensory input, nor do they directly drive motor output --- they are "hidden" somewhere in between. The bulk of the cortex is "hidden" by this definition, and this makes sense if we think of these areas as creating increasingly sophisticated and abstract categories from the sensory inputs, and helping to select appropriate behavioral responses based on these high-level categories. This is what most of the cortex does, in one way or another. These areas have thicker **superficial layers 2,3**, which contain many pyramidal neurons that are well positioned for performing this critical categorization function.
 
-* **Output** areas of cortex have neurons that synapse directly onto muscle control areas ("motor outputs"), and are capable of causing physical movement when directly stimulated electrically. These areas have much thicker **deep layers 5,6**, which send axonal projections back down into many different subcortical areas.
+* **Output** areas of cortex have neurons that synapse directly onto muscle control areas ("motor outputs"), and are capable of causing physical movement when directly stimulated electrically. These areas have much thicker **deep layers 5,6**, which send axonal projections back down into many different subcortical areas. The evolutionarily more ancient mesocortical areas (e.g., cingulate cortex along the medial wall) lack a distinct layer 4, and are primarily output areas with mostly deep layer neurons.
 
 {id="figure_layers-in-hid-out"}
 ![Function of the cortical layers: layer 4 processes input information (e.g., from sensory inputs) and drives superficial layers 2,3, which provide a "hidden" internal re-processing of the inputs (extracting behaviorally relevant categories), which then drive deep layers 5,6 to output a motor response. Green triangles indicate excitation, and red circles indicate inhibition via inhibitory interneurons. Solid lines indicate connections that are included in our models. Dotted lines indicate less strong connections that are not included in our models. BG = basal ganglia which is important for driving motor outputs, and Subcortex includes a large number of other subcortical areas.](media/fig_cortical_layers_in_hid_out.png)

content/evolution.md

@@ -50,6 +50,8 @@
 
 <p id="Alonso-MartinezRubio-TevesCasas-TorremochaEtAl23">Alonso-Martínez, C., Rubio-Teves, M., Casas-Torremocha, D., Porrero, C., & Clascá, F. (2023). Cerebellar and basal ganglia inputs define three main nuclei in the mouse ventral motor thalamus. <i>Frontiers in Neuroanatomy, 17</i>, <a href="https://www.frontiersin.org/journals/neuroanatomy/articles/10.3389/fnana.2023.1242839/full">https://www.frontiersin.org/journals/neuroanatomy/articles/10.3389/fnana.2023.1242839/full</a><a href="http://doi.org/10.3389/fnana.2023.1242839"> http://doi.org/10.3389/fnana.2023.1242839</a></p>
 
+<p id="AltmanBayer15">Altman, J., & Bayer, S.A. (2015). Development of the Human Neocortex. <a href="https://neurondevelopment.org/wp-content/uploads/2015/11/human-neocortical-development-complete.pdf">https://neurondevelopment.org/wp-content/uploads/2015/11/human-neocortical-development-complete.pdf</a></p>
+
 <p id="AlvarezFyffe07">Alvarez, F.J., & Fyffe, R.E.W. (2007). The continuing case for the Renshaw cell. <i>The Journal of Physiology, 584</i>, 31–45. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1113/jphysiol.2007.136200">https://onlinelibrary.wiley.com/doi/abs/10.1113/jphysiol.2007.136200</a><a href="http://doi.org/10.1113/jphysiol.2007.136200"> http://doi.org/10.1113/jphysiol.2007.136200</a></p>
 
 <p id="AnanthRajebhosaleKimEtAl23">Ananth, M.R., Rajebhosale, P., Kim, R., Talmage, D.A., & Role, L.W. (2023). Basal forebrain cholinergic signalling: development, connectivity and roles in cognition. <i>Nature Reviews Neuroscience, </i>1–19. <a href="https://www.nature.com/articles/s41583-023-00677-x">https://www.nature.com/articles/s41583-023-00677-x</a><a href="http://doi.org/10.1038/s41583-023-00677-x"> http://doi.org/10.1038/s41583-023-00677-x</a></p>
@@ -120,6 +122,8 @@
 
 <p id="BaumelJacobsonCohen09">Baumel, Y., Jacobson, G.A., & Cohen, D. (2009). Implications of functional anatomy on information processing in the deep cerebellar nuclei. <i>Frontiers in Cellular Neuroscience, 3</i>, <a href="https://www.frontiersin.org/journals/cellular-neuroscience/articles/10.3389/neuro.03.014.2009/full">https://www.frontiersin.org/journals/cellular-neuroscience/articles/10.3389/neuro.03.014.2009/full</a><a href="http://doi.org/10.3389/neuro.03.014.2009"> http://doi.org/10.3389/neuro.03.014.2009</a></p>
 
+<p id="BayerAltman91">Bayer, S.A., & Altman, J. (1991). <i>Neocortical development. </i> Raven Press New York. <a href="https://neurondevelopment.org/wp-content/uploads/2023/10/1-NCD-front.pdf">https://neurondevelopment.org/wp-content/uploads/2023/10/1-NCD-front.pdf</a></p>
+
 <p id="BayerGiese25">Bayer, K.U., & Giese, K.P. (2025). A revised view of the role of CaMKII in learning and memory. <i>Nature Neuroscience, 28</i>, 24–34. <a href="https://www.nature.com/articles/s41593-024-01809-x">https://www.nature.com/articles/s41593-024-01809-x</a><a href="http://doi.org/10.1038/s41593-024-01809-x"> http://doi.org/10.1038/s41593-024-01809-x</a></p>
 
 <p id="BayerSchulman19">Bayer, K.U., & Schulman, H. (2019). CaM Kinase: Still Inspiring at 40. <i>Neuron, 103</i>, 380–394. <a href="https://www.sciencedirect.com/science/article/pii/S0896627319304866">https://www.sciencedirect.com/science/article/pii/S0896627319304866</a><a href="http://doi.org/10.1016/j.neuron.2019.05.033"> http://doi.org/10.1016/j.neuron.2019.05.033</a></p>