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neuroanatomy1.md
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@@ -4,7 +4,12 @@ Neuroscience is a field of scientific study that seeks to understand how the ner
<img src="figs/human-brain.svg" height="300px">
https://canvas.ucsc.edu/courses/25273
https://canvas.ucsc.edu/courses/36780
<div style="font-size:0.5em;">
<!-- date: -->
</div>
Note:
Welcome. This class will be an Introduction to Neuroscience–
@@ -13,15 +18,15 @@ Neuroscience is a field that by necessity integrates information and techniques
And ultimately it is a field of science that seeks to understand how this lump of biological tissue siting inside our heads has evolved the capability of asking questions about its own nature and existence.
While humankind has learned alot about nervous system structure and function, there is a great deal left to understand. It's up to you to figure it all out.
"carries out *its* **functions**"
Thus it will be you, and your children, and your children’s children that will figure it all out and literally allow human beings to reach the stars.
--
## Syllabus and text book
<div><a href="https://canvas.ucsc.edu/courses/16047/assignments/syllabus">https://canvas.ucsc.edu/courses/16047/assignments/syllabus</a></div>
<div><a href="https://canvas.ucsc.edu/courses/36780/assignments/syllabus">https://canvas.ucsc.edu/courses/16047/assignments/syllabus</a></div>
<div style="width:200px;"><img src="figs/ScreenShot2016-01-04at3.59.29PM_dea1077.png" height="200px"><figcaption>5e 2011</figcaption></div>
@@ -45,7 +50,7 @@ Thus it will be you, and your children, and your children’s children that will
<!-- * Print: `...neuroanatomy1.html?print-pdf` -->
Recommend browser is Firefox or Chrome on a laptop/PC. Some features that only have keyboard bindings (e.g. fullscreen, overview) may not work or be disabled on tablet/touch screen devices.
Recommend browser is Firefox or Chromium on a laptop/PC. Some features that only have keyboard bindings (e.g. fullscreen, overview) may not work or be disabled on tablet/touch screen devices.
</div>
@@ -74,53 +79,55 @@ Therefore the brain’s functions are dynamic, vast and wide ranging, and extend
<div><img src="figs/The_forever_war_1974_1be2645.png" height="200px"><figcaption>J. Haldeman, 1974</figcaption></div>
<!-- <div><img src="figs/ScreenShot2016-01-04at12.58.17PM_e1dcf52.png" height="200px"><figcaption>['Star Trek' Wars, 2008](http://on.cc.com/1r4rOE1)</figcaption></div> -->
<div><img src="figs/ScreenShot2016-01-04at12.58.17PM_e1dcf52.png" height="200px"><figcaption>Futurama, 2008. 'Where no fan has gone before'</figcaption></div>
Note:
Ever since the dawn of the industrial age in the mid 19th century and Jules Verne's 1865 novel 'From the Earth to the Moon' humans have been dreaming of the future, not just here but among the stars. And those futures can become reality like when the Apollo astronauts landed on the moon and acknowledged the inspiration that Verne's orig sci-fi novel had on many.
Neuroscience and its role for proper physiological function is going to play a role in many advances in health and technology for humankind now and far into the future--
* Neuroscience and its role for proper physiological function is going to play a role in many advances in health and technology for humankind now and far into the future--
To reach the stars we will need:
* To reach the stars we will need:
- robots, artificial intelligence, I. Asimov Philip K. Dick's 1968 novel 'Do Androids Dream of Electric Sheep'
- virtual reality, brain machine interfaces, James Cameron's Avatar
- medical tricorders, 1960s series Star Trek
- physiological stasis, cryopreservation, waking up the brain space after travel like Joe Haldeman's 1974 novel 'The Forever War' or the Ridley Scott's movie Aliens
The human brain and its limitless creativity has packed a bunch of computational power into this little device in our pocket. And yet this device is really just made up of lots of simple little semiconductive elements. The human brain even invented this masking tape that currently holds together my broken phone. So what is the atomic unit of our brains function and how is it structured to achieve our cognitive abilities and our consciousness? We will find the answers to some of these question in this course, but will also discover as is usually the case when looking into nature's secrets that we humbly know so little.
The human brain and its limitless creativity has packed a bunch of computational power into this little device in our pocket. And yet this device is really just made up of lots of simple little semiconductive elements. So what is the atomic unit of our brains function and how is it structured to achieve our cognitive abilities and our consciousness? We will find the answers to some of these question in this course, but will also discover as is usually the case when looking into nature's secrets that we humbly know so little.
Or futures that seem impossibly fanciful but who knows 10k or 100k years, maybe consciousness will be woven into some sort of singular virtual world like in the matrix or the cylons from Battle Star Galactica.
Or perhaps a discomforting future where maybe consciousness will be woven into some sort of singular virtual world like in the matrix or the cylons from Battlestar Galactica in ten or ten thousand years?
think of virtual reality which is now almost a reality, can we solve the mismatches between sensory information and body positioning to get rid of the nausea associated with this technology? Think of artifical intelligence and robotics
Think of virtual reality which is now almost a reality, can we solve the mismatches between sensory information and body positioning to get rid of the nausea associated with this technology? Think of artifical intelligence and robotics
If we will be traveling through space we will need to keep our bodies disease free to get wherever we are going-- will be know enough about brain function and neurolgical disease to fix things on the fly with a medical tricorder device like in Star Trek?
Can we read the minds of a suspect in a courtroom with a brain imaging device? Do we even want to do that? Think of Can we rid
The human brain and its limitless creativity has packed a bunch of computational power into this little device in our pocket. And yet this device is really just made up of lots of simple little semiconductive elements. The human brain even invented this masking tape that currently holds together my broken phone. So what is the atomic unit of our brains function and how is it assembled to achieve our cognitive abilities? We will find the answers to some of these question in this course, but will also discover as is usually the case when looking into nature's secrets that we know so little.
If we will be traveling through space (well technically we are already traveling through space;) we will need to keep our bodies disease free to get wherever we are going-- will we know enough about brain function and neurolgical disease to fix things on the fly with a medical tricorder device like in Star Trek?
Can we read the minds of a suspect in a courtroom with a brain imaging device? Do we even want to do that?
Since that time we've dreamed up fantastical futures in shows like Star Trek and the Jetsons and dystopian ones in Blade Runner and the Terminator or even ones past (for example think "long time ago in a galaxy far far away...")
Many of things dreamed of are already presentImagine some of things thought of and now already present flying aeroplanes, personal landspeeders, rocket ships to distant planets
Some of the **things** dreamed of are already present. Flying aeroplanes, personal landspeeders, rocket ships to distant planets, autonomous-automobiles.
- Edgar Rice Burroughs John Carter thought waves example.
Penfield mood organ
- Edgar Rice Burroughs A Priestess of Mars: John Carter hurling thought waves.
- Do Androids Dream of Electric Sheep: Penfield mood organ
* So is the nervous system then a device for
- detecting physiological change?
- seeking pleasurable rewards? a dopamine machine?
- navigating space + time?
- processing emotional secretions?
---
## We will focus on a few basic features of the nervous system
* The mechanisms by which neurons produce signals
* The patterns of connections between nerve cells
* The relationship of different patterns of interconnections to different types of behavior
## Questions to keep in *mind* as we study neuroscience now and beyond
* What signals are produced by a nervous system? How? Why?
* How are input stimuli from the external or internal environment transduced by the nervous system?
* Where and how does sensor input get tranformed into a behavioral decision and an output pattern to be actuated?
* What is a structure? What is a function?
Note:
@@ -143,6 +150,142 @@ sinew
---
## What are brains made of?
A glob of squishy jello? <!-- .element: class="fragment strike" data-fragment-index="1"-->
<figure><img src="figs/image9_e303503.png" height="100px"><figcaption></figcaption></figure>
<figure><img src="figs/image10_c067a0a.png" height="100px"><figcaption></figcaption></figure>
<figure class="fragment fade-in" data-fragment-index="1"><img src="figs/image11_fbb6fc7.png" height="100px"><figcaption>Wikimedia Commons</figcaption></figure>
Cells. (though jello is made of collagen...) <!-- .element: class="fragment fade-in" data-fragment-index="1"-->
Note:
So what are brains made of? Anybody? Jello? What is this 1.5 kg or 3 lb human brain made of?
Yes it is soft and squishy but it is not just a gelanitous mass like jello. Shown here is a section through a human brain. It is about 20 cm long and if we were to zoom in on a tiny part of it and use a special dye and microscope what we see is that the brain is made of cells. So this is a pyramidal neuron in from the cerebral cortex and its cell body is about 30-40µm in diameter.
---
## Brains are made of cells
* Camillo Golgi (Italy)– believed that cells in the brain were directly connected forming a **continuous network** (reticular theory).
* Santiago Ramon y Cajal (Spain)– Brains made up of single cells and communicate at specialized areas called synapses.
* Shared Nobel prize in 1906
Note:
Seems fairly obvious now. But wasn't in the 19th c. Cells widely accepted everywhere else in the 1830’s. But neuroscientists were the last to accept this right up until the turn of the 20th c.
Only after fundamental and rigorous work by these two scientists, C. Golgi and S. Ramon y Cajal in the late 19th c. did we come to appreciate comprised of individual cellular elements rather than a continous network or syncytium.
---
## Golgi staining
Golgi staining: potassium chromate and silver nitrate (1873)
<div><figcaption class="big">Golgi's drawing of the hippocampus impregnated by his stain</figcaption><img src="figs/camillo_golgi_hippocampus_40b7a67.jpg" height="300px"><figcaption>from Golgi's Opera Omnia.</figcaption></div>
<div><figcaption class="big">Golgi's drawing of hippocampal dentate gyrus</figcaption><img src="figs/golgi_nobel_lecture_fig9_eb014b5.png" height="300px"><figcaption>fig. 9 from Golgi's Nobel lecture</figcaption></div>
Note:
Golgi's drawing of hippocampus after performing his black potassum chromate and silver nitrate stain. Bottom is a zoomed in drawing of neurons and their connections in the hippocampal dentate gyrus.
---
## The nervous system is not a syncytium
* syncytium: a mass of cytoplasm with many nuclei but no internal cell boundries
* reticulum: a fine network or netlike structure
* Camillo Golgi, Nobel Lecture December 11, 1906, *The Neuron Doctrine- theory and facts*:
<div style="width:960px; font-size:0.6em">
<div></div>
>"...Far from being able to accept the idea of the individuality and independence of each nerve element, I have never had reason, up to now, to give up the concept which I have always stressed, that nerve cells, instead of working individually, act together, so that we must think that several groups of elements exercise a cumulative effect on the peripheral organs through whole bundles of fibers."
<div>
Note:
Golgi drew the structure of the hippocampus as being all fused together into a reticulum, no free axon endings
Syncytiums are important in living organisms. From the placenta at the beginning of your existence to your multinucleated myocytes and osteocytes that make up your muscle and bones as you chase the Pacific Sun, syncytiums always play an important role.
---
## The Neuron Doctrine
* Santiago Ramon y Cajal
* Neurons are cells. Each is an *individual entity* anatomically, embryologically, and functionally.
* Neurons have a functional polarity
<figure><img src="figs/cajal_retina_bff166d.jpg" height="300px"><figcaption>Cajal drawing of golgi stained retina. Cells are separate units and arrows indicate direction of information flow.</figcaption></figure>
Note:
Neurons in culture have specific endings. EM methods, dye filling experiments.
Heinrich Wilhelm Gottfried von Waldeyer-Hartz (6 October 1836 – 23 January 1921) was a German anatomist and conceived the word 'neuron'.
Golgi in his nobel lecture:
>(3) The neuron is a physiological unit. This fundamental idea which Waldeyer expressed with perfect precision has been enlarged upon both from anatomical and functional sides with additional propositions, for example : **The communication between neurons is only established by casual contact. There is scarcely any nervous tissue apart from the neurons; the neurons are also trophic units.**
individual entitites. boxes within boxes. containers.
---
## The Nobel Prize in Physiology or Medicine 1906
>"in recognition of their work on the structure of the nervous system"
<div style="width:300px; float:left;"><img src="figs/CamilloGolgi_5c05797.jpg" height="200px"><figcaption class="big">
Camillo Golgi
Pavia University
Pavia, Italy
</figcaption></div>
<div style="width:600px; float:left;"><img src="figs/SantiagoRamonyCajal_dd682a4.jpg" height="200px"><figcaption class="big">
Santiago Ramón y Cajal
Madrid University
Madrid, Spain
</figcaption></div>
Note:
---
## How many neurons in a human brain?
* 100 thousand
* 10 million
* 100 million
* 1 billion
* 10 billion
* 100 billion <!-- .element: class="fragment highlight-green" -->
* 1 trillion
Note:
- in cerebral cortex humans generally have most neurons, where we have about 20 billion. Even compared to an elephant that has 3 times the number of overall neurons. Though some species of cetaceans (whales and dolphins) approach the number of our cortical neurons and recent research has shown that the long-finned pilot whale likely has more neurons in its cerebral cortex than we do.
---
## The nervous system and its function is the product of both our genes and our environment
<div style="font-size:0.9em">
@@ -155,7 +298,7 @@ sinew
Note:
* Neuroscience encompasses many fields: genetics, molecular and cell biology, developmental biology, physiology.
* Neuroscience encompasses many fields: genetics, molecular and cell biology, developmental biology, physiology, physics, electrical engineering, computer science.
- not nature or nurture, nature and nurture
- language, learning to ride a bike
@@ -242,136 +385,6 @@ But most single gene mutations do not cause such drastic effects, with a more su
---
## What are brains made of?
A glob of squishy jello? <!-- .element: class="fragment strike" data-fragment-index="1"-->
<figure><img src="figs/image9_e303503.png" height="100px"><figcaption></figcaption></figure>
<figure><img src="figs/image10_c067a0a.png" height="100px"><figcaption></figcaption></figure>
<figure class="fragment fade-in" data-fragment-index="1"><img src="figs/image11_fbb6fc7.png" height="100px"><figcaption>Wikimedia Commons</figcaption></figure>
Cells. (though jello is made of collagen...) <!-- .element: class="fragment fade-in" data-fragment-index="1"-->
Note:
So what are brains made of? Anybody? Jello? What is this 1.5 kg or 3 lb human brain made of?
Yes it is soft and squishy but it is not just a gelanitous mass like jello. Shown here is a section through a human brain. It is about 20 cm long and if we were to zoom in on a tiny part of it and use a special dye and microscope what we see is that the brain is made of cells. So this is a pyramidal neuron in from the cerebral cortex and its cell body is about 30-40µm in diameter.
---
## Brains are made of cells
* Camillo Golgi (Italy)– believed that cells in the brain were directly connected forming a **continuous network** (reticular theory).
* Santiago Ramon y Cajal (Spain)– Brains made up of single cells and communicate at specialized areas called synapses.
* Shared Nobel prize in 1906
Note:
Seems fairly obvious now. But wasn't in the 19th c. Cells widely accepted everywhere else in the 1830’s. But neuroscientists were the last to accept this right up until the turn of the 20th c.
Only after fundamental and rigorous work by these two scientists, C. Golgi and S. Ramon y Cajal in the late 19th c. did we come to appreciate comprised of individual cellular elements rather than a continous network or syncytium.
---
## Golgi staining
Golgi staining: potassium chromate and silver nitrate (1873)
<div><figcaption class="big">Golgi's drawing of the hippocampus impregnated by his stain</figcaption><img src="figs/camillo_golgi_hippocampus_40b7a67.jpg" height="300px"><figcaption>from Golgi's Opera Omnia.</figcaption></div>
<div><figcaption class="big">Golgi's drawing of hippocampal dentate gyrus</figcaption><img src="figs/golgi_nobel_lecture_fig9_eb014b5.png" height="300px"><figcaption>fig. 9 from Golgi's Nobel lecture</figcaption></div>
Note:
Golgi's drawing of hippocampus after performing his black potassum chromate and silver nitrate stain. Bottom is a zoomed in drawing of neurons and their connections in the hippocampal dentage gyrus.
---
## The nervous system is not a syncytium
* syncytium: a mass of cytoplasm with many nuclei but no internal cell boundries
* reticulum: a fine network or netlike structure
* Camillo Golgi, Nobel Lecture December 11, 1906, *The Neuron Doctrine- theory and facts*:
<div style="width:960px; font-size:0.6em">
<div></div>
>"...Far from being able to accept the idea of the individuality and independence of each nerve element, I have never had reason, up to now, to give up the concept which I have always stressed, that nerve cells, instead of working individually, act together, so that we must think that several groups of elements exercise a cumulative effect on the peripheral organs through whole bundles of fibers."
<div>
Note:
Golgi drew the structure of the hippocampus as being all fused together into a reticulum, no free axon endings
---
## The Neuron Doctrine
* Santiago Ramon y Cajal
* Neurons are cells. Each is an individual entity anatomically, embryologically, and functionally.
* Neurons have a functional polarity
<figure><img src="figs/cajal_retina_bff166d.jpg" height="300px"><figcaption>Cajal drawing of golgi stained retina. Cells are separate units and arrows indicate direction of information flow.</figcaption></figure>
Note:
Neurons in culture have specific endings. EM methods, dye filling experiments.
Heinrich Wilhelm Gottfried von Waldeyer-Hartz (6 October 1836 – 23 January 1921) was a German anatomist and conceived the word 'neuron'.
Golgi in his nobel lecture:
>(3) The neuron is a physiological unit. This fundamental idea which Waldeyer expressed with perfect precision has been enlarged upon both from anatomical and functional sides with additional propositions, for example : **The communication between neurons is only established by casual contact. There is scarcely any nervous tissue apart from the neurons; the neurons are also trophic units.**
---
## The Nobel Prize in Physiology or Medicine 1906
>"in recognition of their work on the structure of the nervous system"
<div style="width:300px; float:left;"><img src="figs/CamilloGolgi_5c05797.jpg" height="200px"><figcaption class="big">
Camillo Golgi
Pavia University
Pavia, Italy
</figcaption></div>
<div style="width:600px; float:left;"><img src="figs/SantiagoRamonyCajal_dd682a4.jpg" height="200px"><figcaption class="big">
Santiago Ramón y Cajal
Madrid University
Madrid, Spain
</figcaption></div>
Note:
---
## How many neurons in a human brain?
* 100 thousand
* 10 million
* 100 million
* 1 billion
* 10 billion
* 100 billion <!-- .element: class="fragment highlight-green" -->
* 1 trillion
Note:
- in cerebral cortex humans generally have most neurons, where we have about 20 billion. Even compared to an elephant that has 3 times the number of overall neurons. Though some species of cetaceans (whales and dolphins) approach the number of our cortical neurons and recent research has shown that the long-finned pilot whale likely has more neurons in its cerebral cortex than we do.
---
## Glial cells
Glia
@@ -591,7 +604,7 @@ Note:
Note:
Polarity is everywhere in physics... and biology!
Polarity is everywhere and is everything, in physics... and biology!
* electric dipole moments of molecules
* earth's magnetic poles
@@ -750,7 +763,7 @@ Note:
Note:
?Grab Coombs et al., 2006 figures...
todo: need Coombs et al., 2006 figures...
---
@@ -787,7 +800,7 @@ Affect vs effect
---
## Neurons communicate by electricity
## Neurons communicate with electrical pulses
* Axons project great distances
* Use action potentials to transmit information
@@ -797,6 +810,8 @@ Affect vs effect
Note:
What is electricity? It's energy. It's variance. From the flow of electric charge across a conducting medium.
--