diff --git a/2016-09-17-lecture01.md b/2016-09-17-lecture01.md
index 8079354..e515e7b 100644
--- a/2016-09-17-lecture01.md
+++ b/2016-09-17-lecture01.md
@@ -1,60 +1,84 @@
-##What is neuroscience?
+## What is neuroscience?
-Neuroscience is a field of scientific study that seeks to understand how the nervous system carries out its functions and what goes wrong when it doesn’t. While we understand much about nervous system function, there is much to learn. You are the scientists who will figure it all out.
+Neuroscience is a field of scientific study that seeks to understand how the nervous system carries out its functions and what goes wrong when it doesn’t.
-[President Obama brain initiative](http://abcnews.go.com/Politics/video/obama-says-brain-initiative-will-be-transformative-18861944)
+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.
http://courses.pbsci.ucsc.edu/mcdb/bio125/
Note:
-Welcome. This class will be an Introduction to Neuroscience– Neuroscience is a field that by necessity integrates information and techniques from many other scientific disciplines— not just biological sciences like genetics, molecular biology, biochemistry, immunology, physiology. But also physics, engineering, computer science, psychology. And these days neuroscience is touching upon fields as varied as sociology, criminology, marketing, ethics, and the law. So what is Neuroscience? Neuroscience is fundamentally a field that…
+Welcome. This class will be an Introduction to Neuroscience– Neuroscience is a field that by necessity integrates information and techniques from many other scientific disciplines— not just biological sciences like genetics, molecular biology, biochemistry, immunology, physiology. But also physics, engineering, computer science, psychology. And these days neuroscience is touching upon fields as varied as sociology, criminology, marketing, ethics, and the law. So what is Neuroscience? Neuroscience is fundamentally a field that...
+
+And ultimately it is a field of science that seeks to understand how a lump of biological tissue siting inside our heads has evolved the capability of asking questions about its own nature.
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 or save us from the cylons on battlestar galactica, whichever comes first. And hopefully recent funding initiatives will help in this cause.
+--
+
+## Site keyboard bindings
+
+* Navigate: *arrow keys* and *spacebar*
+* Fullscreen: *f*
+* Overview: *o* or *esc*
+* Zoom object: *alt/option–click*
+
+
+
---
-##What are the nervous system’s functions?
+## What are the nervous system’s functions?
-* The nervous system organizes and controls an individual’s appropriate interactions with the environment.
-* Thus, it’s functions are dynamic, vast and wide-ranging – extending to include all thoughts, perceptions, bodily actions, behaviors, and even the very essence of one’s being: consciousness and the mind.
-
-['Star Trek' Wars](http://on.cc.com/1r4rOE1)
-
-http://courses.pbsci.ucsc.edu/mcdb/bio125/
-
-
+* The nervous system organizes and controls an individual’s appropriate interactions with the environment
+* Thus, it’s functions are dynamic, vast and wide-ranging – extending to include all thoughts, perceptions, bodily actions, behaviors, and even the very essence of one’s being: consciousness and the mind
Note:
-What does the nervous system do? It organizes and controls an individuals interactions with the environment. It does this by processing current or past experiential information and making and executing behavioral decisions.
+What does the nervous system do? It organizes and controls an individuals interactions with the environment. It does this by processing current or past experiential information and making and executing behavioral decisions.
+Therefore the brain’s functions are dynamic, vast and wide ranging, and extends to include all thoughts, perceptions, and actions and the very core of what it means for each of one us to be us–– consciousness and the mind. It is this complex lump of biological tissue, this emergent computational system that allows us humans to not only imagine the future, but to create it as well.
+--
-Therefore the brain’s functions are dynamic, vast and wide ranging, and extends to include all thoughts, perceptions, and actions and the very core of what it means for each of one us to be us–– consciousness and the mind. It is this complex lump of biological tissue, this emergent computational system that allows us humans to not only imagine the future, but to create it as well.
+## Neuroscience and the future of humankind
-
-
----
-
-
-##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.
-
-[http://courses.pbsci.ucsc.edu/mcdb/bio125/](http://courses.pbsci.ucsc.edu/mcdb/bio125/)
-
-
+
+['Star Trek' Wars](http://on.cc.com/1r4rOE1)
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
+
+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
+\
+
+- Edgar Rice Burroughs John Carter thought waves example.
+
+
---
-##The nervous system and its function is the product of both our genes and our environment
+
+## 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
+
+
+
+Note:
+
+
+---
+
+## The nervous system and its function is the product of both our genes and our environment
+
+
+
* We are now in a gene-centric “post-genomic” phase of neuroscience
* Human genome sequenced- approximately 20,000 genes.
@@ -62,181 +86,197 @@ Note:
* Mice, flies, and worms have nervous systems and even express many of the same genes as humans. Genetics allows us to correlate gene activity with nervous system function.
* Neuroscience therefore encompasses many fields, including genetics, cell biology, physiology, and development biology.
+
+
Note:
-…
---
-##Genome size does not correlate with nervous system complexity
+## Genome size does not predict nervous system complexity
-100,000,000,000
+
+
-71,000,000
+organism | # of genes | # of base pairs | # of neurons | development time (young adult)
+---------- | ---------- | --- | ------------ | -------------------------
+*Caenorhabditis elegans* (nematode) | ~19,000 | ~97 million | 302 | 8 hrs
+*Drosophila melanogaster* (fruit fly) | ~15,000 | ~120 million | ~250,000 | 7–11 days
+*Danio rerio* (zebrafish) | ~24,000 | ~1.5 billion | ~10,000,000 | 30 days
+Mouse | ~25,000 | ~3.5 billion | ~71,000,000 | 2-3 months
+Human | ~20,000 | ~3.5 billion | ~100,000,000,000 | 18 years
+African elephant | ~20,000 | ~3.1 billion | ~267,000,000,000 | 18 years
-302
+
-10,000,000
-
-250,000
-
-Number of
-
-neurons in whole nervous system
-
-
+
Note:
Number of genes is not related to nervous system complexity or size. The nematode c. elegans has just 302 neurons, and yet its genome contains virtually as many genes as a humans. An african elephant brain weighs 3 times more than a human brain and has 3 times the number of neurons.
-
-
The largest brains are those of sperm whales, weighing about 8 kg (18 lb). An elephant's brain weighs just over 5 kg (11 lb), a bottlenose dolphin's 1.5 to 1.7 kg (3.3 to 3.7 lb), whereas a human brain is around 1.3 to 1.5 kg (2.9 to 3.3 lb). Brain size tends to vary according to body size.
+* Drosophila 7-11 days (28-34degs C)
+* zebrafish 3-4 days juvenile swimming and visual behavior. young adult at 3 mo. full adult at 6 mo.
+* genome sizes at http://www.biology-pages.info/G/GenomeSizes.html
+
---
-##There are many brain-specific and non-brain specific genes expressed in the nervous system
+## There are many brain-specific and non-brain specific genes expressed in the nervous system
+
+Neuroscience 5e Fig. 1.1
-
Note:
-There are many genes are expressed only in the brain, but there are many genes expressed in the brain that are not specific to only the nervous system.
+Out of those 20000 genes, there are many expressed genes that are common between the nervous system and other tissues, however there is also a substantial fraction that are expressed specifically in the nervous system
---
-##A single mutation can lead to dramatic brain size defects
+## A single mutation can lead to dramatic brain size defects
Mutation in a spindle pole gene call ASPM1
-
+Neuroscience 5e Fig. 1.1
+
Note:
Now mutations in single genes in the right place in our genome can cause drastic effects on the formation of our brain’s wiring.
-
-
For example, shown here is a person with a mutation in ASPM1 a protein used to make spindle poles for mitotic stem cells during embryonic development.
-
-
But most single gene mutations do not cause such drastic effects, with a more subtle and complex set of genetic and environmental risk factors causing neurological disease, similar to and probably exceeding the complex etiology of cancer.
+
---
-##Model organisms— C. Elegans
+## Model organisms— C. elegans
-* It is hard to visualize and monitor neurons and manipulate genes in humans so neuroscientists study a number of different organisms.
-* Worm nervous system highlighted with green fluorescent protein (GFP): 302 cells
+* It is hard to visualize and monitor neurons and manipulate genes in humans so neuroscientists study a number of different organisms
+* The nematode worm *C. elegans* is great for genetic engineering and has a tiny nervous system (just 302 neurons)
+
+
C. elegans– commons.wikimedia.org/w/index.php?curid=2680458
+
+
C. elegans wiring diagram– [openworm.org](http://www.openworm.org), neuroconstruct.org
-
Note:
+C. elegans is a nematode or roundworm. It is non-infectious and non-parasitic organism just 1 mm long and it can be easily genetically engineered. That means you can introduce mutations to genes or express fancy inert proteins that allow you to track the function of genes and cells in living animals making it a great model organism. For neuroscientists it has 302 total neurons making it a great model organism.
+
Now to do neuroscience research we have to use model organisms of course. Small number of neurons, can be labeled using GFP or other means. Many mutant worms have been isolated that affect nervous system function.
+However, we have more than a million neurons that just form the optic nerve from each of our eyes!
+
+
---
-##Model organisms— Mus. Musculus
+## Model organisms— squid
+
+Squids have unusually large axons (1 mm diameter)
+
+
20000 Lieues Sous les Mers, J. Verne
+
+
Atlantic squid, *Loligo pealei*
+
+
+
+
+Note:
+
+Jules Verne provided inspiration for the space age
+
+Phylum: Mollusca
+Class: Cephalopoda
+Order: Teuthida
+Family: Loliginidae
+Genus: Loligo
+
+Atlantic squid (Loligo pealei)
+
+Phylum: Mollusca
+Class: Cephalopoda
+Order: Sepiida
+Family: Sepiidae
+Genus: Sepia
+
+
+Other important invertebrate organisms in neuroscience research include sea slugs and fruit flies.
+
+---
+
+
+## Model organisms— Mus. musculus
The mouse is a common model in neuroscience research
-[http://www.youtube.com/watch?v=5D7bbyguACI](http://www.youtube.com/watch?v=5D7bbyguACI)
+
Common house mouse *Mus. musculus*, jax.org
-
+
Mouse brain 3D rendering, [Brain Explorer 2](http://mouse.brain-map.org/static/brainexplorer)
-
+
Green labeled neurons inside a mouse brain
Note:
+* Mouse brain is about 2 cm in length
+* genetically tractable
+* [https://www.youtube.com/watch?v=stPThgZ2Y5o](https://www.youtube.com/watch?v=stPThgZ2Y5o)
---
-##Model organisms— squid
-Squids have unusually large axons
-
-1 mm
-
-
-
-
-
-Note:
-
-jules verne
-
----
-
-##Model organisms
+## Model organisms– other mammals
Higher mammals are used to study more complicated brain functions
-
+
-
Note:
-Research with cats was critical for work from the 1950s to 1980s that allowed neuroscientist to learn how visual signals are processed in the highests circuits of the mammalian brain.
-
-
-
-And research with monkeys has been really essential for learning about perceptual, attentional, and decision making in the mammalian brain.
-
+Research with cats was critical for work from the 1950s to 1980s that allowed neuroscientist to learn how visual signals are processed in the highest circuits of the mammalian brain.
+And research with rhesus monkeys has been essential for learning about perceptual, attentional, and decision making in the mammalian brain together with research into brain-machine interfaces that have direct clinical applications for human patients.
+3rs: Replacement, Reduction, and Refinement
---
-##Brain lesion patients
+## Brain lesion patients
-* Lesions in brains or degenerative diseases help us understand brain functi* Phineas Gage- Railroad spike through frontal lobes changed his personality.
+* Lesions in brains or degenerative diseases help us understand brain function
+* Phineas Gage– Railroad spike through frontal lobes changed his personality
-
+
-
+
Note:
Furthermore, studies of patients with brain lesions has historically been key to localizing parts of the brain that affect emotional states and learning and memory.
-
-
e.g. Phineas Gage in 1848 his whole personality changed after the spike went through his brain.
-
-
-Harlow wrote: “the equilibrium ... between his intellectual faculties and his animal propensities seems to have been destroyed”
-
-
-
+Harlow wrote: “the equilibrium... between his intellectual faculties and his animal propensities seems to have been destroyed”
---
-##What are brains made of?
+## What are brains made of?
+
+So what are brains made of? A glob of squishy jello?
-Note:
-
-So what are brains made of? Is it just a glob of squishy jello?
-
-
-
----
-
-##What are brains made of?
-
-
-
Wikimedia Commons
-
@@ -245,26 +285,26 @@ Note:
Yes— but this tissue is some pretty complicated soft tissue. The answer is the brain is made of cells.
-
-
Shown here is a section through a human brain. If we zoom in on a tiny part of it
+
---
-##How many neurons in a human brain?
+## How many neurons in a human brain?
* 100 thousand
* 10 million
* 100 million
* 1 billion
* 10 billion
-* 100 billion
+* 100 billion
+* 1 trillion
Note:
---
-##Brains are made up of cells
+## Brains are made of cells
* Camillo Golgi (Italy)– believed that cells in the brain were connected forming a continuous network (reticular theory).
* Santiago Ramon y Cajal (Spain)– Brains made up of single cells-communicate at specialized areas called synapses.
@@ -276,21 +316,26 @@ Cells widely accepted everywhere else in the 1830’s. Neuroscientists last to
---
-##The Nobel Prize in Physiology or Medicine 1906
+## The Nobel Prize in Physiology or Medicine 1906
-"in recognition of their work on the structure of the nervous system"
+>"in recognition of their work on the structure of the nervous system"
+
+
Camillo Golgi
Pavia University
Pavia, Italy
+
+
+
+
Santiago Ramón y Cajal
Madrid University
Madrid, Spain
-
+
-
Note:
@@ -298,7 +343,7 @@ Note:
---
-##Golgi staining
+## Golgi staining
Golgi staining: potassium chromate and silver nitrate (1873)
@@ -316,7 +361,7 @@ Top golgi stain of a cortex at different magnifications, bottom is a drawing of
---
-##Is the nervous system a syncytium?
+## Is the nervous system a syncytium?
* syncytium: a mass of cytoplasm with many nuclei but no internal cell boundries
* Answer: NO!
@@ -334,7 +379,7 @@ Golgi drew the structure of the hippocampos as being all fused together into a r
---
-##The Neuron Doctrine
+## The Neuron Doctrine
* Santiago Ramon y Cajal
* Neurons are cells. Each is an individual entity anatomically, embryologically, and functionally.
@@ -348,7 +393,7 @@ Neurons in culture have specific endings. EM methods, dye filling experiments.
---
-##Two basic cell types in the nervous system
+## Two basic cell types in the nervous system
* Neurons and Glia
@@ -358,7 +403,7 @@ Note:
---
-##Glia
+## Glia
* Outnumber neurons by 10-50 fold
* myelin sheath
@@ -367,63 +412,38 @@ Note:
* structural support for neurons
* critical role in brain development
-
-
Note:
greek for ‘glue’
---
-##Types of glial cells
+## Types of glial cells
-* Microglia- phagocytes, mobilized after infection, injury, or disease
-* Macroglia- three types
-* Astrocytes– CNS, most numerous type of glia and contain star shaped long processes.
-* Oligodendrocytes– Myelin producing cells of the CNS.
-* Schwann cells– Myelin producing cells of the PNS.
+
+
+
+* Astrocytes– Support cells of the CNS, most numerous type of glia and contain star shaped long processes
+* Microglia- CNS macrophages. Act as phagocytes, mobilized after infection, injury, or disease
+* Oligodendrocytes– Myelin producing cells of the CNS
+* Schwann cells– Myelin producing cells of the PNS
* Satellite cells– Support cells of the PNS
-Note:
+
