A new beginning!

Good morn, good eve, good night, my fellow tumblpeeps.

Tumblr informs me that this is my 199th blog post. I really don’t think I’m going to be posting any more under this title. I’ll leave the blog active for now as a few people are still sharing round some posts, but consider this my goodbye as a pure neuroscientist.

BUT!! Do not despair, I am moving my shit over to my new blog…


On which I hope to be providing (amateur) help for people looking to get into medicine and detailing my horrendous days of continual revision and brain-pain.

Hope to see you on the other side.


It’s all over

My 3 years studying undergraduate neuroscience are over, and I haven’t been truly sober since Wednesday. Now for a few months of buffer time, followed by 4 years of graduate entry medicine. During which time, I promise my tumblr activity shall increase. Starting today. Productive times ftw.


“24 hours and 20 minutes, then degree is finished…”

Gearing up for 200th post

To my small (yet growing) army of minions:

Any suggestions as to what I should do to mark this occasion?


Visual Processing (Part 3)

FINALLY we get to the level of the cortex. It is here that the horribly, horribly complicated events of cortical processing occur. The primary visual cortex (V1/Striate cortex) is located at the very back of the brain and is the first stopping point for most visual information. Some information is sent directly to the superior colliculus, this is involved in involuntary control of saccades.

Structure of the primary visual cortex

As with the rest of the cortex, the information from the sensory input arrives in layer 4 of the cortex (though some neurons have been shown to terminate in layers 3/2). The magnocellular pathway terminates in layers 4B and 4Cα and the parvocellular pathway in layers 4A and 4Cβ. From here, the information is passed up and down cortical layers in series. This, however, is not the end of the story by far.

Detecting colour in V1

V1 can be divided into a number of distinct processing areas. Arguably one of the most histologically characteristic elements of V1 are theblobs. These are so called as they are an easy to recognise patterned set of structures seen when stained by cytochrome oxidase. Neuronal labelling has shown that P and K pathway neurons terminate in the blobs. Current research, however, has shown that M pathway neurons also have input into the blobs. If this pathway is cooled (and therefore neuronal action is reduced) the firing rate in the blobs decrease to induced stimuli. This, however, is not reciprocated with the P pathway in interblobs, suggesting M pathway dominance, and going against the Hubel and Livingstone hypothesis that the M and P pathways are totally distinct throughout the visual pathway (Hubel and Livingstone, 1987).

The P pathway carries red and green colours and the K pathway blue and yellow. The blobs can therefore be seen to be the site of initial colour processing in the visual cortex. The majority of connections from the blobs are sent to the ventral stream (read two stream hypothesis for more information) which is argued to be the pathway which deals with colour and form.

The functional organisation of the visual cortex is not simply divided into colour and non-colour. Each blob lies within a column of alternating ocular dominance, i.e. each column is under control of one eye over the other, though both input to all columns. Each column also has a particular orientation. This is where the clever shit happens. I should also point out that here V1 is a site of both parallel and serial processing

Detecting lines in V1

Detection of lines in V1 begins with bars. Each receptive field (which is still maintained all the way from the RGCs, established by the bipolar cells) associates withsimplecells. If a bar is detected in a specific orientation, the simple cells of that orientation fire. If not, they don’t this paralell processing of information enables a detection of lines, and thus the beginning of encoding the visual world can occur.

These simple cells join together to fire on complex, then hypercomplex cells. This is the true division of parallel and serial processing in the visual cortex.

There is some evidence to suggest that both texture and motion can also be processed in V1.

From V1 to the rest of the brain

From V1, the visual information is dealt with according to what it comprises of. The two streams hypothesis covers this nicely; the dorsal stream detects motion and the ventral detects colour and form. V3 interacts with both streams.

It is obvious that the visual system cannot be truly divided into either paralle or serial processing. If anything, this is an outdated and outmoded approach to studying vision in old world primates. The pathways converge after become truly distinct, yet remain seperate throughout the process.

An interesting paper by Bullier and Nowak (1995) stated that parts of the visual cortex were neither parallel nor serial with regard to processing. The latencies between visual areas in response to evoked stimuli were far too short to be considered a result of serial processing, and there was no true parallel processing in the system either, it all intermingles far too much.

So there you have it. That’s what I’m writing tomorrow in my exam. Plus some embellishments that I couldn’t be bothered to add. Hopefully these three posts will take me about two hours to write in the exam hall, otherwise I predict bad shit will happen.


Oh, and if I don’t survive,


Kissing Hank’s Ass - a tale of evangelical religion

John: "Hi! I’m John, and this is Mary."

Mary: "Hi! We’re here to invite you to come kiss Hank’s ass with us."

Me:   "Pardon me?! What are you talking about? Who’s Hank, and why would I want to kiss His ass?"

John: "If you kiss Hank’s ass, He’ll give you a million dollars; and if you don’t, He’ll kick the shit out of you."

Me:   "What? Is this some sort of bizarre mob shake-down?"

John: "Hank is a billionaire philanthropist. Hank built this town. Hank owns this town. He can do whatever He wants, and what He wants is to give you a million dollars, but He can’t until you kiss His ass."

Me:   "That doesn’t make any sense. Why…"

Mary: "Who are you to question Hank’s gift? Don’t you want a million dollars? Isn’t it worth a little kiss on the ass?"

Me:   "Well maybe, if it’s legit, but…"

John: "Then come kiss Hank’s ass with us."

Me:   "Do you kiss Hank’s ass often?"

Mary: "Oh yes, all the time…"

Me:   "And has He given you a million dollars?"

John: "Well no. You don’t actually get the money until you leave town."

Me:   "So why don’t you just leave town now?"

Mary: "You can’t leave until Hank tells you to, or you don’t get the money, and He kicks the shit out of you."

Me:   "Do you know anyone who kissed Hank’s ass, left town, and got the million dollars?"

John: "My mother kissed Hank’s ass for years. She left town last year, and I’m sure she got the money.”

Me:   "Haven’t you talked to her since then?"

John: "Of course not, Hank doesn’t allow it."

Me:   "So what makes you think He’ll actually give you the money if you’ve never talked to anyone who got the money?"

Mary: "Well, He gives you a little bit before you leave. Maybe you’ll get a raise, maybe you’ll win a small lotto, maybe you’ll just find a twenty-dollar bill on the street."

Me:   "What’s that got to do with Hank?"

John: "Hank has certain ‘connections.’"

Me:   "I’m sorry, but this sounds like some sort of bizarre con game."

John: "But it’s a million dollars, can you really take the chance? And remember, if you don’t kiss Hank’s ass He’ll kick the shit out of you."

Me:   "Maybe if I could see Hank, talk to Him, get the details straight from Him…"

Mary: "No one sees Hank, no one talks to Hank."

Me:   "Then how do you kiss His ass?"

John: "Sometimes we just blow Him a kiss, and think of His ass. Other times we kiss Karl’s ass, and he passes it on."

Me:   "Who’s Karl?"

Mary: "A friend of ours. He’s the one who taught us all about kissing Hank’s ass. All we had to do was take him out to dinner a few times."

Me:   "And you just took his word for it when he said there was a Hank, that Hank wanted you to kiss His ass, and that Hank would reward you?"

John: "Oh no! Karl has a letter he got from Hank years ago explaining the whole thing. Here’s a copy; see for yourself."

From the Desk of Karl

  1. Kiss Hank’s ass and He’ll give you a million dollars when you leave town.
  2. Use alcohol in moderation.
  3. Kick the shit out of people who aren’t like you.
  4. Eat right.
  5. Hank dictated this list Himself.
  6. The moon is made of green cheese.
  7. Everything Hank says is right.
  8. Wash your hands after going to the bathroom.
  9. Don’t use alcohol.
  10. Eat your wieners on buns, no condiments.
  11. Kiss Hank’s ass or He’ll kick the shit out of you.

Me:   "This appears to be written on Karl’s letterhead."

Mary: "Hank didn’t have any paper."

Me:   "I have a hunch that if we checked we’d find this is Karl’s handwriting."

John: "Of course, Hank dictated it."

Me:   "I thought you said no one gets to see Hank?"

Mary: "Not now, but years ago He would talk to some people."

Me:   "I thought you said He was a philanthropist. What sort of philanthropist kicks the shit out of people just because they’re different?"

Mary: "It’s what Hank wants, and Hank’s always right."

Me:   "How do you figure that?"

Mary: "Item 7 says ‘Everything Hank says is right.’ That’s good enough for me!"

Me:   "Maybe your friend Karl just made the whole thing up."

John: "No way! Item 5 says ‘Hank dictated this list himself.’ Besides, item 2 says ‘Use alcohol in moderation,’ Item 4 says ‘Eat right,’ and item 8 says ‘Wash your hands after going to the bathroom.’ Everyone knows those things are right, so the rest must be true, too.”

Me:   "But 9 says ‘Don’t use alcohol.’ which doesn’t quite go with item 2, and 6 says ‘The moon is made of green cheese,’ which is just plain wrong."

John: "There’s no contradiction between 9 and 2, 9 just clarifies 2. As far as 6 goes, you’ve never been to the moon, so you can’t say for sure."

Me:   "Scientists have pretty firmly established that the moon is made of rock…"

Mary: "But they don’t know if the rock came from the Earth, or from out of space, so it could just as easily be green cheese."

Me:   "I’m not really an expert, but I think the theory that the Moon was somehow ‘captured’ by the Earth has been discounted*. Besides, not knowing where the rock came from doesn’t make it cheese.”

John: "Ha! You just admitted that scientists make mistakes, but we know Hank is always right!"

Me:   "We do?"

Mary: "Of course we do, Item 7 says so."

Me:   "You’re saying Hank’s always right because the list says so, the list is right because Hank dictated it, and we know that Hank dictated it because the list says so. That’s circular logic, no different than saying ‘Hank’s right because He says He’s right.’"

John: "Now you’re getting it! It’s so rewarding to see someone come around to Hank’s way of thinking."

Me:   "But…oh, never mind. What’s the deal with wieners?"

Mary: She blushes.

John: "Wieners, in buns, no condiments. It’s Hank’s way. Anything else is wrong."

Me:   "What if I don’t have a bun?"

John: "No bun, no wiener. A wiener without a bun is wrong."

Me:   "No relish? No Mustard?"

Mary: She looks positively stricken.

John: He’s shouting. “There’s no need for such language! Condiments of any kind are wrong!”

Me:   "So a big pile of sauerkraut with some wieners chopped up in it would be out of the question?"

Mary: Sticks her fingers in her ears.”I am not listening to this. La la la, la la, la la la.”

John: "That’s disgusting. Only some sort of evil deviant would eat that…"

Me:   "It’s good! I eat it all the time."

Mary: She faints.

John: He catches Mary. “Well, if I’d known you were one of those I wouldn’t have wasted my time. When Hank kicks the shit out of you I’ll be there, counting my money and laughing. I’ll kiss Hank’s ass for you, you bunless cut-wienered kraut-eater.”

Just to say that this comes from http://www.jhuger.com/kisshank.php and is not my own work, I just thought it would amuse y’all.

Copyright © 1996 - 2005 James Huber


Visual Processing (Part 2)

The visual information arrives at the thalamus, the brain’s glorified relay station. 

"No processing can go on here!" I hear you cry…

Midget retinal ganglion cells (mRGCs) synapse in the top 4 layers, containing the parvocellular neurons. Parasol RGCs synapse in the bottom 2 layers, the magnocellular neurons. The small, bistratified RGCs synapse between, in the koniocellular layer.


Layers 1, 4 and 6 come from the opposite eye (contralateral) and 2, 3 and 5 come from the eye the same side as this LGN (ispsilateral). It should also be said at this point that the magnocellular (M) pathway contains the rod photoreceptor information (presence of light/dark, movement, shape etc.), the parvocellular (P) pathway contains red/green cone information and the koniocellular (K) pathway contains blue cone information.

These pathways are anatomically and functionally distinct and remain so until they reach the visual cortex. This is the prime example of parallel processing in the visual system, the information is dealt with along three individual streams until it reaches a termination in the visual cortex. The process of ‘labelled lines’ - tracing neuronal tracts through the brain with a radiolabel/tracer - has shown that the neurons from the RGCs remain within the three tracts all the way back to the cortex.


Arse biscuits.

I was working on visual processing 2 and 3 and they now appear to have vanished.

Let the table-flipping commence.

Triple-wielding the face pens. Bring on the knowledge.
NB. I have not had a stroke. I’m pulling a sexy face.

Triple-wielding the face pens. Bring on the knowledge.


NB. I have not had a stroke. I’m pulling a sexy face.


Visual Processing (Part 1)

When we talk about visual processing, or ‘processing’ in general in the central nervous system, it’s easy to get confused as to what this term means.

To ‘process’ something, at a basic level, is to sort information, categorise it and pass it on through relevant channels. It’s not an end point, it’s a part of a process,  the middle of a flow diagram. This is essentially what the CNS does, it takes information and channels it through correct pathways, which builds up to form a bigger system. For those who think that this is a far too simple perspective, look at your computers. Sorting information is basically all your CPU is doing right now. And look! Your screen is showing you the deep blue of the tumblr background! Headphones are outputting Rise Against, The Beatles, or even Pink Floyd (but only if you have impeccable taste).

The visual system processes in two fashions, parallel and serial (hierarchical). These coming posts will detail processing at both levels, all the way from the retina to the visual cortex and beyond. In this first post, we’ll look at the fundamental processing of visual information, in the retina.


Visible light is nothing more than electromagnetic radiation with a wavelength between 380nm and 760nm. Anything above or below this specific portion of the EM spectrum is invisible to the human eye. Light between these two wavelengths enters the eye and passes to the rods and cones of the retina. Within the rods and cones, phototransduction occurs. Photons of a specific wavelength isomerise 11-cis retinal to all-trans retinal, causing a conformational change in the opsin molecule to which the retinal molecule is bound. The opsin molecule is a membrane-bound G-protein coupled receptor (a signal transduction molecule allowing for small changes to result in large molecular effects). This change causes a downstream reduction in levels of the molecule cyclic GMP.

Photoreceptor cells have a very strange property; they fire when inactive, a phenomenon called a ‘dark current’ (a current is produced in the absence of photostimulation). This current is generated by cGMP-gated sodium channels. This then follows that light causes these channels to close, and the dark current to switch off. This then causes a drop in neurotransmission between the photoreceptor and the next cell in the chain, the bipolar cell. Although glutamate is normally considered to be excitatory, in this case a decrease in the EAA allows the bipolar cell to depolarise, passing the ‘light present’ signal to the retinal ganglion cells. 

The above two paragraphs don’t describe processing, they describe encoding. The initial processing step here occurs at the level of the bipolar cell. Through reading some of the literature, it becomes quite apparent that there are two sorts of encoding at the level of the retina, through receptive field processing and initial pathway divergence.

1. Receptive fields

The receptive fields of the retinal ganglion cells (RGCs) can be attributed to the interaction of horizontal and bipolar cells. These connecting bipolar neurons between the photoreceptors which encode and the ganglion cells which transduce, band the photoreceptors together into groups, creating a receptive field. Horizontal and amacrine cells (modified glial cells) introduce a process known as lateral inhibition, which will be explained below.

The typical receptive field of the RGC is circular, and divided into two. There are two kinds of receptive field, on-centre and off-centre. To put it simply, take an on-centre field. When light falls onto photoreceptors within the inner circle, the on-centre RGC fires. If light falls outside of the circle, or encompasses the circle, the on-centre RGC does not fire (or fires weakly and is not detected).

This initial encoding allows for downstream effects in the visual cortex to occur, which will be dealt with in the next part. It also shows some initial encoding of sensory information; visual stimuli are immediately divided into two pathways, on- and off-centre. This forms the very basis of object detection.

2. Initial pathway division

The RGCs are immediately assigned a destination. By the process known as labelled lines (injecting a retrograde tracer/dye into the neuron and following the pathway to map the tracts) the information divergence has been shown to act at the level of the retina.

Midget ganglion cells take encoded information to the parvocellular pathway through the dorsal area of the lateral geniculate nucleus (LGNd).

Parasol ganglion cells take information to the magnocellular pathway of the LGNd.

Small, bistratified cells also go to the LGNd, but take cells via the koniocellular pathway.

Photosensitive ganglion cells use melanopsin as a photopigment and go to the suprachiasmatic nucleus, amongst other areas of the brain, to regulate circadian rhythmicity (in layman’s terms, they help reset the ‘bodyclock’).

This division of labour amongst the neurons shows how encoding is immediately followed by the transfer of neural information into the correct and appropriate pathways necessary for further packaging of information. This may well be considered to be a method of parallel processing, as information is dealt with simultaneously. The process of generating the on-centre and off-centre receptive fields is not, however, as it involves transfer of information in series, including the regulating inhibitory inputs of the surrounding cells.

And if you can make head or tail of any of that, you’re a better person than me.


From the thalamus to the cortex and cortical processing!


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