Thursday, November 12, 2009

Bistable Anatomy

In the rat thalamus, each whisker is represented by a chunk of tissue known as a 'barreloid'. The following image is Figure 12c from Haidarliu and Ahissar (2001) Size Gradients of Barreloids in the Rat Thalamus. It is a drawing of a large chunk of a rat's brain, with the location of the barreloids indicated by the cuboid shape:

Where, exactly, are the barreloids? Perceptually the cube is bistable, a Necker cube the solid lines either representing the cube's front face or back face. It could drive an anatomist crazy! (Note: 'L' stands for 'lateral' and 'R' stands for 'rostral').

While the figure is perceptually ambiguous, it is clear from the paper that they follow the convention that solid lines are to be interpreted as in the front. Also, based on an informal poll of people in my lab, it seems most people lock in on the "correct" perceptual interpretation initially.

Monday, November 09, 2009

Barrel Cortex Overview

The barrel cortex roughly corresponds to the primary somatosensory cortex of rodents. It has become a standard model system for the study of cortical structure, function, and development. It's the system where I spend most of my life as a postdoc.

Fox's book Barrel Cortex is the best overview that I have seen. It is unfortunately much too costly for out-of-pocket purchase (140 bucks), but your library may have a copy.

Wednesday, September 23, 2009

Consciousness (8): From perception to interpretation

Number eight in my series of posts on consciousness. All the posts are indexed here.

The previous two posts were a tour of ambiguous visual stimuli. Let's use these data to generate ideas about consciousness. Ideally, these ideas will lead to prediction-generating hypotheses about consciousness and clarify the explanatory target for neuroscience.

Interpreting Necker
Let's jump-start our thinking with a familiar example: your experience of the Necker Cube (shown on the right). This time, try looking at it with one eye. You should still experience perceptual bistability.

People seem to naturally gravitate toward describing bistable perception as an alternation between two different interpretations of a stimulus. The psychologists that study bistable perception do the same. For instance, Suzuki and Peterson (2000) say:
Bistable displays are displays that afford at least two potential interpretations even though the physical displays remain unchanged. [...] At any given moment, only one interpretation of a bistable display is seen; over time, the two perceptual interpretations spontaneously and stochastically alternate.
How are we to interpret the view that the brain interprets a stimulus? Is it a metaphor? If so, is it useful? Let's start by considering the nature of interpretation more generally, independently of the issue of conscious perception.

What is interpretation?
In general, to interpret something is to determine what it means. We are probably most aware of the need for an interpretation when we encounter difficult bits of writing. What fan of JRR Tolkien hasn't struggled to interpret Bilbo's pronouncement to his fellow Hobbits, "I like less than half of you half as well as you deserve"? What the heck does that mean?

Interpreting a complicated text can be a painstaking process that often requires a good deal of specialized knowledge. People build careers on their ability to interpret confusing legalese, complex poems, or arcane works of philosophy. Some philosophers are infamous for the patience and charity required to construct an intelligible interpretation of their work. For example, the oft-revered philosopher Ludwig Wittgenstein (1922) wrote, 'The thing is independent, in so far as it can occur in all possible circumstances, but this form of independence is a form of connexion with the atomic fact, a form of dependence.' Most readers will probably agree that it is hard to interpret Wittgenstein's sentence, that the meaning is not transparent.

While our need to interpret text is most obvious when we encounter tortured prose, technically speaking we interpret even the clearest expressions. The meaning of the sentence, 'George Washington was the first President of the United States,' is fairly transparent to most Americans. That is, interpreting the sentence is effortless, given our background knowledge. For someone just learning English, or someone with no knowledge of the United States, the sentence's meaning will not be so clear. For some philosophers, the meaning of the above quote from Wittgenstein might seem transparent. Transparency of meaning is not an intrinsic feature of a chunk of text, but depends on the background knowledge we bring to the text.

We have to be careful, as some texts might not mean anything, or if they do it might not be worth the effort to decipher them. Chomsky (1957) produced the famous sentence, 'Colorless green ideas sleep furiously' as an example of grammatically well-formed nonsense. Of course, we could generate grammatically ill-formed nonsense too: 'Gorp dilettante achieve on.' Whether such strings are literally meaningless is an interesting philosophical question that we won't explore. I include this discussion partly to highlight that I have been throwing around the term 'meaning' without defining it, a point we will revisit in the next post.

So far I've focused on interpreting expressions in natural language. However, people also interpret paintings, dreams, medical test results, pretty much anything. Psychologists used to be quite fond of asking people to interpret random smears of ink on sheets of paper (the Rorschach test). While these cases are interesting, to keep the discussion more manageable, in the next post I'll focus on the analogies between perception and interpretation of expressions in natural language.

With this rudimentary understanding of interpretation in hand, in the next post we will consider ways in which perception and interpretation are similar. While I will ultimately eschew thinking of perception as literally identical to interpretation, it is an analogy worth mining for ideas about conscious visual perception.

Chomsky (1957) Syntactic Structures Mouton, The Hague/Paris.

Suzuki and Peterson (2000) Multiplicative effects of intention on the perception of bistable apparent motion, Psychological Science 11: 202–209.

Wittgenstein, L (1922) Tractatus Logico-Philosophicus (Ogden translation) Cosimo Classics.

Table of Contents of posts on consciousness.

Thursday, September 10, 2009

Consciousness (7): More Ambiguous Figures

The seventh in my series of posts on consciousness. All the posts are indexed here.

In this post we'll finish the tour, started in the previous post, of ambiguous figures.

Some of the most compelling illusions include things that move. Indeed, every time we watch a movie we succumb to the illusion of apparent motion. As we saw in the previous post, a rotating Necker Cube evokes vivid bistability. The present group of ambiguous figures include moving parts that are essential for the illusion.

Ambiguous structure from motion
The following video looks like a cylinder rotating either clockwise or counterclockwise (its direction is bistable). There is no cylinder drawn in the video, just a bunch of randomly placed spots. The spots' motion is set to match the velocity they would have if painted on the surface of a cylinder, and this motion signal alone is enough to give the impression of a particular shape.

It sometimes takes more than 30 seconds for the percept to switch, so you might need to watch the movie more than once. I am able to make it reverse faster by rotating my finger around the bottom of the imaginary cylinder as if I were pushing it in a new direction.

Bistable See-Saw
In the following animation, the barbell-shaped object should look like it is flipping back and forth like a see-saw. Sometimes the see-saw crosses through the horizontal axis, and other times the vertical axis. You might even see the barbell rotating 'round and 'round in a circle, though in my experience this is rare.

ambiguous dumbell

I lock in fairly strongly to the horizontal see-saw, but when I cover up the bottom half of the image for a few seconds, this brings out the other percept.

One Plaid or Two Gratings?
Stare at the black dot in the following animation. While initially you probably see a plaid pattern moving upward, you will eventually see two translucent sinusoidal patterns (often described as 'gratings') sliding past one another. It took me almost 30 seconds the first time before the percept switched, so stick with it.

One plaid or two gratings?

The Spinning Girl
One of my favorite illusions. This beautiful ballerina was created by Nobuyuki Kayahara. In which direction is the ballerina doing her pirouette? Most people see her rotating clockwise initially, but the stimulus is actually ambiguous, so you can also see her rotating counterclockwise.

If you have trouble getting her to switch directions, cover her body and look only at the shadows at the bottom of the image. With the number of cues reduced, you should be able to see the shadow change direction. Once that happens, slowly lift your hand while maintaining the new direction of rotation to reveal the new pirouette direction.

This illusion has been misinterpreted as a test of handedness, or a test of whether you are right-brained or left-brained. There is no evidence for these claims, and I'm not sure where the rumors originated.

Binocular rivalry
Binocular rivalry has been a workhorse for the study of consciousness. This is partly because, in addition to the extensive psychological studies of binocular rivalry, neuroscientists have locked onto rivalry as a model for the study of the neural basis of consciousness. While we'll look more deeply at rivalry in future posts, for now we'll treat it as just another cool bistable percept.

To experience rivalry in the following image, put a piece of paper perpendicular to the screen between the two images, so your left eye sees the face and your right eye sees the house (your face should be about six inches from the screen). Be sure to fuse the checkered circles in the center of each figure. Once you obtain fusion, hold it for a while and you will experience rivalry.

Most people do not see a simple fusion of the house and face, but rather the patterns alternate. For instance, you might see the house for a few seconds, and then the face will dominate for a while, and so on. That is binocular rivalry. During transitions, the new percept will spread across the old in a kind of traveling wave, in which case you might see a dynamic quilt-like pattern.

Ambiguous forms
In this class of ambiguous figures, perception alternates between often drastically different types of objects (e.g., face and vase). These illusions are probably better known than all of the others. They are used in advertisements and art, and there are so many on the internet that I can only show a tiny sample. I won't say much about them, as the titles suggest what the two objects are supposed to be, and most of them aren't very difficult to see.

Vase versus Face
The old standby in every introductory psychology textbook.

Duck versus Rabbit
Another classic. I like the following version (from Torrey (1970)) because the two interpretations seem equally likely.

Wife/Mother-in-law and Husband/Father-in-law
On the top is a beautiful young socialite and a nasty witch-like banshee. Below is a handsome gadabout and a wretchedly distasteful lecher.

Chef versus Dog
Tilt your head to the left to see the dog, and to the right to see the goofy French chef.

Nude woman versus Reagan face

Kissing Jesters
It alternates between a single jester facing you, and two jesters facing each other, their lips lightly touching.

Gypsy versus Narcissist
The top of the image shows the ambiguous version, while the bottom shows disambiguated versions (gypsy on the left and narcissistic woman looking into the mirror on the right).

Man's face or Woman Reading?
Our last figure. I would be remiss, in a tour of ambiguous forms, if I didn't pay homage to the great surrealist Salvador Dali. His paintings are filled with beautiful and sometimes hauntingly plastic forms. The following painting, 'The Image Disappears,' was painted by Dali in 1938.

It seems somehow appropriate to let Salvador Dali be the last stop in our tour of ambiguous figures. If you have any favorites that I haven't included, please let me know in the comments or via email.

Where we are headed
While ambiguous images are intrinsically cool, they also provide a window into the nature of visual consciousness. Based on these illusions, in the next post I'll make some general hypotheses about the nature of (visual) perception. These hypotheses will give us a target for the neuronal data, to which we will then turn.

Sources of Illusions
The structure-from-motion demo is supplementary material in Krug et al. (2008). The Bistable See-Saw is adapted from the ambiguous quartet illusion, which was described by Ramachandran and Antsis (1985) (a tactile version is described in Carter et al. (2008)). The plaid/grating illusion is from Stoner et al (1990). The Spinning Girl was created by Nobuyuki Kayahara, who works in digital design. The house-face image used for binocular rivalry is from Tong et al. (1998). Vase/face goes back to Rubin (1915), but the one here is from Fischer (1967). The duck-rabbit was published originally by Jastrow (1899), but the one here is from Torrey (1970). The mother-in-law/wife image was originally published by Hill (1915), and the husband/father-in-law was originally published in Botwinick (1961). Kissing Jesters is from Fisher (1967). Chef/Dog is from Wallach and Austin (1954). Nude/Reagan is from Fisher (1968), a paper that shows 30 ambiguous forms from the history of psychology. Gypsy/Narcissist is from Fisher (1967).

Botwinick (1961) Husband and father-in-law: A reversible figure. American Journal of Psychology, 74: 312-313.

Carter, O, Konkle, T, Wang, Q, Hayward, V, and Moore C (2008) Tactile Rivalry Demonstrated with an Ambiguous Apparent-Motion Quartet. Current Biology 18: 1050-1054.

Fisher, G (1967), Measuring Ambiguity, American Journal of Psychology 80: 541-557.

Fischer, G (1968) Ambiguity of form: Old and new. Perception and Psychophysics 4: 189-192.

Hill, We (1915) My wife and my mother-in-law. Puck November 6.

Jastrow, J. (1899) The Mind's Eye. Popular Sci. Monthly, 54: 299-312.

Kristine Krug, Emma Brunskill, Antonina Scarna, Guy M Goodwin, Andrew J Parker (2008) Perceptual switch rates with ambiguous structure-from-motion figures in bipolar disorder. Proc. R. Soc. B, 275: 1839-1848.

Ramachandran, V.S., and Anstis, S.M. (1985). Perceptual organization in multistable apparent motion. Perception 14, 135-143.

Rubin, EJ (1915) Synsopleved Figurer: Studier i psykologisk Analyse. [If anyone has the full reference please let me know]

Stoner, GR, Albright TD, and Ramachandran VS (1990) Transparency and coherence in human motion perception. Nature 344: 153-5.

Tong, Nakayama, Vaughan, and Kanwisher (1998) Binocular rivalry and visual awareness in human extrastriate cortex, Neuron 21: 753–759

Torrey, CC (1970) Trace Localization and the Recognition of Visual Form. The American Journal of Psychology, 83: 591-600.

Wallach, H, and Austin, P (1954) Recognition and the localization of visual traces. Am J Psychol, 67:338-40.

Table of Contents of posts on consciousness.

Saturday, September 05, 2009

Consciousness (6): Reversible Figures

The sixth in my series of posts on consciousness. All the posts are indexed here.

Background: Why do we need psychology?
Instead of just diving into the neural data, let's take some time to examine our target, consciousness. Clarifying the features of conscious awareness will provide a more precise target for our neuronal theories.

The ultimate goal is to develop an understanding of consciousness at both the neuronal and psychological levels. The two approaches should coevolve until they fit together as nicely as our ideas about trait inheritance and DNA, as well as our ideas about action potential generation and single channel biophysics.

To flesh out the analogy with inheritance/DNA, let's consider the work of Gregor Mendel. By controlling the reproduction of different strains of pea plants, Mendel was able to measure many features of inheritance well before anybody had heard of DNA. His work provided an explanatory target for molecular biologists who unraveled the mechanisms only much later. Similarly, psychologists have gained quite a bit of knowledge of consciousness by simply studying consciousness, knowledge gained without focusing much at all on the specific neuronal mechanisms involved.

There are literally thousands of psychological experiments and clinical studies that reveal interesting features of consciousness. Obviously, we'll only be able to look at a tiny subset of these data. This means I'll need to curate the data with some caution: I must be wary of cherry picking, or focusing only on data that lets me push some pet theory. The right approach toward any pet hypothesis is to try to kill it with data. We should actively seek out falsifying evidence, not data that confirms what we already believe.

We have to start somewhere in this galaxy of data, so let's begin with a set of illusions that has entertained and puzzled psychologists, and the general public, for nearly 200 years: ambiguous stimuli. I start with them partly for their cocktail party value, but also because they are an excellent gateway into the psychology of conscious perception.

Ambiguous Visual Stimuli and Bistable Perception
A stimulus is ambiguous when it can evoke different percepts. That is, even though the stimulus is unchanging, our experience of the stimulus oscillates between two "interpretations." The alternating perceptual experiences are known as bistable percepts. (If this is confusing, hold on: many examples are coming up).

In this post I'll focus on cases in which the percepts switch back and forth between two identical objects (e.g., two cubes) that are seen from two different perspectives. They are often called 'reversible figures.'

Necker cube
The Necker Cube is probably the most famous reversible figure. It was first discussed in print in 1832 by a Professor of Minerology, LA Necker (Necker, 1832). The Necker Cube is at the top of the following figure. Looking at the line drawing tends to evoke alternating experiences of two cubes. These cubes are shown, in an unambiguous form, below the Necker Cube.

Perceptually, one of the cubes appears to come out of the page pointing down toward the left (the pink cube on the left), while the other cube appears to come out of the page pointing up to the right (the pink cube on the right).

While most people's visual system automatically generates a percept of one of the cubes (an amazing fact in itself), some people tend to stay locked into one interpretation. That is, they don't spontaneously experience bistability. If this is you, just keep staring and your percept will eventually switch. The longer you look at a reversible figure, the more frequently the perceptual alternation will occur.

Reversible Steeple
It is relatively easy to generate ambiguous drawings similar to the Necker Cube: make a line drawing of an arbitrary 3-D polygon and it is likely to generate bistable percepts. For instance, here is a five-sided solid, the Reversible Steeple:

One of the steeples points toward you (with the rectangular base further away), while the other points away (its base will be closer to you).

Schröder's Staircase
The following figure should appear as a set of steps with either the blue or the pink "wall" closer to you.

When the red wall is closest, it seems you are looking at a staircase from above (the more standard perspective such as when you are approaching a set of stairs to climb). When the blue wall appears closest, it will seem as if you are looking up at a staircase from underneath, or an upside-down staircase, or an overhanging unfinished brick wall (the latter two descriptions are from Wallin's book).

Plush Chair
You can imagine the following is one of those plush velvet chairs with brass buttons on the front and back.

One percept is of a chair facing you: you see the chair from above with the backrest facing you and the seat of the chair is coming out toward you. The other percept is of a chair facing away from you: you see the chair from below, with the back of the backrest facing you and the seat is going away from you.

Inverting Hairbrush
It appears to be a hair brush. It can appear either with the bristles facing you, or the bristles facing away.

Scripture's Blocks
This is one of my favorite reversible figure in this post, one of the more vivid cases of bistability. The image should appear as a set of long rectangular blocks stacked upon each another.

In one percept, each block is oriented down to the left, capped on the bottom by a white face. The hatched shading is the top surface of each block. In the other percept, each block is oriented up to the right with its white face at the top. In this case, the hatched shading coats the front surface of each block.

The scope of perceptual reorganization
I'll finish by illustrating the deep and sometimes startling nature of the perceptual reorganization during alternation. We'll look at two modifications of the Necker Cube.

Arrowhead Cube
I've placed two arrows on the "surface" of the Necker Cube below. Consider two questions. Are the arrows on the inside or outside surface of the cube? In what direction are the arrows pointing? As you probably guess, the answer depends on which cube you see!

When you see the down-left cube, then the arrows appear on the outside of the cube, and seem to point toward you. However, when you see the top-right cube, they appear to be painted on the inside surface of the cube, and to point backwards away from you.

Somehow, when the brain alternates between cubes, it takes note of additional features of the cube and integrates them into the percept in an appropriate way. It does this without you having to think about it, without you consciously knowing how you do it.

Rotating Necker Cube
The final bistable percept is my favorite of the bunch, the Rotating Necker Cube. It is a picture of a cube that is rotated by the same amount (in the same direction) with each time step. You should see a rotating cube. Does the cube still show bistability even when rotating?

Not only does the Rotating Necker Cube still alternate, but when it alternates it reverses its apparent direction of rotation! Once the percept switches, our visual system interprets the exact same movement as rotation in the opposite direction.

I will be devoting a future post to the Necker cube, as it is such a rich source of ideas and data.

Where we are headed
In the next post (maybe even two) we'll continue looking at ambiguous stimuli. This post has been a quick list of reversible figures, without much theory or discussion of consciousness. We will ultimately use these illusions to brainstorm about the nature of visual consciousness. Then we'll have something more precise that we can target from a neuronal perspective.

Philosophical dessert
Just as Mendel's laws were consistent with many possible molecular mechanisms, these visual illusions are consistent with any number of lower-level neuronal explanations. For that matter, the illusions considered in isolation are consistent with dualism (roughly speaking, dualists believe that the mind is not part of nature, that it is a different kind of thing altogether such as a soul). Illusions provide useful data that all people (not just neurophiles like myself) interested in consciousness should struggle to explain. Dualists of the world, get off of your armchairs!

Original Sources of Illusions
The Reversible Steeple is adapted from John Wallin's wonderful monograph Optical Illusions of Reversible Perspective published in 1905 (it is available free at Google Books). Schröder's staircase was first published in Schröder (1858). I got the idea for coloring the two walls of the staircase from, a site full of optical illusions. The Inverting Hairbrush and Plush Chair are both adapted from Wallin (1905). Scripture's blocks were introduced by Scripture (1897), though the figure used above is taken from Wallin (1905). The Arrowhead Cube is adapted from Mason et al. (1973).

I am not sure who first noticed bistability in the Rotating Necker Cube. If anyone knows the background, please let me know. Wallin (pages 46-47) says Wheatstone looked at moving Necker Cubes, but it seems Wheatstone just held wire cubes in his hand and contemplated them while he moved them about (see Wheatstone (1838)). Neither Wheatstone nor Wallin remarked on the apparent reversal of rotation, so the first observation was likely after the publication of Wallin's monograph in 1905.

Mason, J, Kaszor, P, and Bourassa, C.M. (1973) Perceptual structure of the Necker cube. Nature 244: 54-56.

Necker, LA (1832) Observations on some remarkable Optical Phænomena seen in Switzerland; and on an Optical Phænomenon which occurs on viewing a Figure of a Crystal or geometric Solid. The London and Edinburgh Philosophical Magazine and Journal of Science (3rd Series) 1, No 5, 329-337.

Schröder, H (1858) Über eine optische Inversion bei Betrachtung verkehrter, durch optische Vorrichtung entworfener physischer Bilder. Annalen der Physik und Chemie 181: 298-311. [Note last name sometimes spelled 'Schroeder' or 'Schroder']

Scripture, E.W. (1897) The New Psychology. Walter Scott Ltd, London.

Wallin, J.E.W. (1905) Optical Illusions of Reversible Perspective: A volume of historical and experimental researches. Stanton Call Press, Stanton IA.

Wheatstone, C (1838) Contributions to the Physiology of Vision.—Part the First. On some remarkable, and hitherto unobserved, Phenomena of Binocular Vision. Philosophical Transactions of the Royal Society of London, 128: 371 - 394.

Table of Contents of posts on consciousness.

Friday, August 28, 2009

The Necker Prism

To prepare the next installment in my series on consciousness research, I've been studying the Necker Cube. Little did I know that the cube was actually a prism that displays the main threads of perception research since 1833. An entire book could easily be written about this simple little line drawing. Despite all the research, there are still basic questions about the cube that haven't been addressed experimentally. I'll post what I've learned in the next couple of weeks.

Sunday, August 16, 2009

Consciousness: Table of Contents

This post will be a permanent placeholder for links to all of my consciousness posts. It will expand until I finish posting on the topic.

(1) Creationists take aim at consciousness: It begins by mentioning that the Creationists have finally discovered consciousness, but mostly focuses on why real scientists should take consciousness seriously as an object of (scientific) study.

(2) Introducing Mr B: A look at the methods of your garden-variety biologist, and what distinguishes a biological approach from other perspectives (like that of the physicist).

(3) Mr B's first take on consciousness: In his first look at the evidence, Mr B concludes that neuronal processes are necessary and sufficient for consciousness in humans.

(4) Leveling with Mr B: We examine the different spatial and temporal levels of organization in the nervous system, and pinpoint the levels most relevant for consciousness.

(5) Switching Voices: Discusses the reasons I will begin referring to Mr B in the first person.

(6) Reversible Figures: Shows and discusses several reversible figures to illustrate perceptual ambiguity and bistable perception.

(7) More Ambiguous Figures: finishing our tour of ambiguous visual stimuli.

(8) From perception to interpretation: starts to explore the claim that perception involves stimulus interpretation. Focus is on determining just what interpretation is.

(9) From texts to the grotesque cinema: to help make precise the claim that perception is stimulus interpretation, we examine the question, 'What is a stimulus?' in some detail.

(10) Contents and Vehicles: starts exploring the analogies between linguistic interpretation and visual perception. First up: there is a content/vehicle distinction.

(11) Ambiguity and context: a continuation of post 10. I examine ambiguity and contextual influences in perception and language interpretation.

(12) What the brain thinks it knows: continuing the previous two posts. I examine the effects of background knowledge and assumptions in perception and language interpretation.

(13) The interpreter versus the scribe: summary of the view that perception is stimulus interpretation.

(14) Interpretation mechanics: Discussion of the view that perception involves unconscious inference. Representations introduced.

(15) Opening the time capsule: quotations, from some great thinkers, that tie together the previous nine posts.

Thursday, August 06, 2009

Consciousness (5): Switching Voices

An intermezzo in my series of consciousness posts. It's been a while since I posted, so I needed to oil the chain.

In conversations about consciousness, the voice of the garden-variety biologist (Mr B) often gets drowned out. This is typically due to blithely confident philosopher-types who act as if the armchair provides just as much authority as the lab bench when it comes to consciousness. Equally perplexing is that some folk's confidence actually becomes bolstered by the paucity of theoretically significant experimental results about consciousness. A lack of data makes good scientists less confident, not more confident, about a topic. (There are interesting parallels with creationism here.)

I am happy to start by inverting this antiscientific bias about consciousness. In that spirit, I will grant Mr B sole control of the lectern until he has finished saying what he has to say. Only then will I entertain questions from those armchair pilots who believe they have deadly objections to Mr B's project. At that point we will be better posed to see if they are right.

While I am not Mr B, for the above reasons I do consider myself his advocate. Because it is becoming a distraction to talk about him in the third-person, I will simply speak in his voice for a bit. Because confusion is likely to follow such a grammatical shift, this post will serve as a handy reference (especially for those tempted to bemoan my ignorance of what the philosophers have (putatively) contributed to our understanding of consciousness).

Next up, we'll get back to the science.

Wednesday, February 25, 2009

Nature Trifecta

A big day for systems neuroscience in Nature yesterday: three papers! Each paper investigates a different question about synaptic organization in the cortex. Not one paper created a new word ending in '-omics,' an auspicious sign.

I superficially describe the main results from each paper below, with some figures.

First, Brown and Hestrin bring us Intracortical circuits of pyramidal neurons reflect their long-range axonal targets. After fluorescent labeling of corticocortical (CC), corticostriatal (CS), and corticotectal (CT) pyramidal cells in cortex, they sliced the mouse brain and patched onto as many as four of the cells in layer five of V1 to measure the probability of cells synapsing onto cells of the same type (and later in the paper, different types).

They found distinct patterns of connectivity for the different cell types (see Figure). For instance, while 20 percent of the CS cells were connected monosynaptically, CT pyramidal cells only hooked up with one another about five percent of the time. They further showed this wasn't merely because some cells are more promiscuous than others (though they didn't show this for CS neurons).

Next up was a paper from Murayama and others in Larkum's group titled Dendritic encoding of sensory stimuli controlled by deep cortical interneurons. They loaded layer V cells in rat somatosensory cortex with calcium indicator, and then imaged layer 1-3 calcium activity during hindlimb stimulation. The supragranular signals represent activity solely in the apical dendrites from the loaded Layer 5 pyramidal cells. Via various pharmacological manipulations (often involve injecting more boluses into layer V), as well as in-vitro patch clamps, they support the claim that a particular type of inhibitory interneuron in layer V suppresses dendritic calcium levels. Then, using triple patch clamp (two neighboring layer V pyramidal cells, and one of their dendrites), they showed that stimulating one of the cells produced dendritic inhibition in the other cell via a disynaptic connection.

Of the three papers, this would be the best one to present in a journal club because it is fairly complicated and hard to understand on a quick once-through. A journal club audience would appreciate you doing the work for them. Frankly, I still haven't thought through the logic of all their experimental manipulations.

Third, from Petreanu and others in Svoboda's group is The subcellular organization of neocortical excitatory connections. It was only a matter of time before the channel rhodopsins spawned acronyms. In this quite elegant paper they described their application of sCRACM [subcellular ChR2-assisted circuit mapping] to determine the spatial organization of axodendritic synapses onto neurons in somatosensory cortex of mice. They did this in slices in which particular areas expressed channel rhodopsin ChR2. For instance, they expressed ChR2 in the VPM nucleus of the thalamus, which carries information to the whisker barrels in S1. Then they could stimulate the axons of the VPM neurons with a laser to find its postsynaptic targets.

They patched onto a cell in S1, and would then laser-stimulate the channelrhodopsin-expressing axons in the vicinity of the patched neuron. When the HH channels were blocked, a laser pulse on a ChR2-expressing axon would still generate PSPs in the postsynaptic cell. The spatial resolution of the mapping was approximately 60 um2, so they were able to map the distribution of synapses with decent precision. The figure accompanying this paragraph is an activation map of a layer 5B pyramidal cell in which the ChRs were expressed in the VPM nucleus of the thalamus. Most of the VPM->S1 synapses occur in Layers IV and VB, though there is some activity in supragranular layers.

The second and third papers use very cool methods to achieve fairly unsurprising results. The first paper used more common methods, but the results were a bit more interesting (i.e., less predictable). All in all, a good week for synapses.

Friday, February 13, 2009

Happy Birthday, Darwin

Why not read something cool about evolutionary biology in honor of one of our greatest naturalists?

Some good online reading:
*Darwin: an online exhibit from the American Museum of Natural History.
*15 Evolution Gems: beautiful piece put together by Nature discussing 15 papers published in their journals that provide striking examples of evolutionary thinking. Unfortunately no figures.
*Evolution 101: A nice introductory course put together at Berkeley.

Good books:
*Frogs, flies, and dandelions: a book that focuses on what we know, and don't know, about speciation.
*How and why species multiply: a great book on speciation using Darwin's finches as a case study. Written by two monsters in the field.
*Evolution of Nervous Systems: an amazing four-volume set edited by Kaas. Too expensive to buy, but you should be able to find chapters online through your library. Check this link to see if you have access from your IP address.
*Endless forms most beautiful: a wonderful introduction to the hot new science of evo-devo (evolutionary developmental biology).

Friday, January 23, 2009

Consciousness (4): Levelling with Mr B

Mr B has hypothesized that the brain is necessary and sufficient for conscious experience in humans (and probably other animals). The brain, unfortunately for Mr B, is an incredibly complex object. It consists of multiple interdependent processes that operate across different spatial and temporal scales.

Spatial scales in the brain
The left-hand side of the figure below lists neuronal processes that operate at different spatial scales (spatial scale increases as you go down the figure). Associated with each level of organization are experimental techniques typically used to access the phenomena at that level. A few of these techniques are listed to the right of each level.

Measurements at a lower-level are often used to help illuminate what is going on in higher levels. For instance, there are many studies that correlate single cell responses with behavior. A detailed anatomical characterization of individual cells slowly builds up a picture of the distribution and abundance of neuronal cell types in the entire brain.

While the techniques used at higher levels typically don't reveal the details of the lower-level processes (e.g., fMRI does not tell you what is happening in an individual neuron), the data from higher levels do provide useful clues about the functional roles of the lower level phenomena. For instance, behavioral studies can suggest how individual motor neurons help to govern behavior. This is important because, as we discussed before, part of Mr B's job as a biologist is to discover the function of the mechanisms he is studying. Just as you won't understand the biological role of sperm by focusing narrowly on how a sperm locomotes, it is not possible to understand the function of an individual neuron without studying its role in the neural network in which it is embedded, and ultimately the role of this network in behavior.

Temporal scales
As spatial scales increase, the relevant temporal scales also tend to increase. This is because the higher-level processes emerge from the interaction of many events at lower levels. For instance, a single action potential lasts about a millisecond, so network dynamics take place on longer time scales (network dynamics require presynaptic action potential propagation, neurotransmitter release, and postsynaptic responses often in a large number of neurons).

Note this positive correlation between spatial scales and temporal scales is not a hard and fast rule. There are lower-level molecular processes that can take longer than minutes to unfold, for instance.

At what level is consciousness?
At what level(s) of organization should Mr B begin his investigation of consciousness? This is not something that can be decisively answered a priori. He needs to dive in and do some experiments to discover the spatiotemporal organization of processes in the conscious brain. We will visit many of the techniques and levels of organization in the above chart as we follow Mr B.

However, Mr B knows enough neuroscience to form tentative hypotheses about the levels of organization required for consciousness. For instance, it is quite unlikely that a single neuron is sufficient for consciousness. This would be a brittle way to build an important process into the brain. This means that we should be looking at the level of the neural network or higher for the neural signatures of consciousness.

On the other hand, we know that the entire brain is not necessary for consciousness. People lose bits of their brain all the time (e.g., car accidents and strokes) without losing consciousness. Further, it is clear that behavior isn't constitutive of conscious experience. We can be paralyzed by curare but still conscious, and when we dream our motor system is effectively shut down but we still have experiences.

Hence, somewhere between small neural networks and areas/nuclei in the levels chart are the most likely candidates to find processes essential to consciousness. This suggests the time-scales of the processes should be relatively long (i.e., longer than the millisecond scale at any rate).

Minimal basis for consciousness
Mr B can use the above discussion to put a finer point on his working hypothesis from the previous post (namely, the brain is necessary and sufficient for consciousness in humans). Because the entire brain isn't necessary and sufficient, there must be some subset of the brain that is. It could be a certain set of cortical areas and subcortical nuclei. It could be the entire cortex, or perhaps just the brain stem. We just don't know right now. But what Mr B is after is this minimal subset of neuronal processes that is necessary and sufficient for consciousness.

Behavior and consciousness
Perhaps paradoxically, while Mr B doesn't think behavior is constitutive of consciousness, the most direct experimental indicators of consciousness he has are behavioral. That is, the best way to find out if someone is aware of something is to ask them if they see (or feel, or hear) it. There is presently no foolproof neuronal measure of conscious experience. While Mr B does think that such a measure should exist, it is something we will have to discover by doing the science.

The good news and the bad news for Mr B
That consciousness seems to be a higher-level phenomenon makes it both easier and harder to study. Mostly harder. The good news is that most of the techniques targeted at lower levels can be used to study consciousness, such as single cell recordings. And of course, those techniques developed to record larger-scale activity, such as fMRI, may also be revealing. This is useful because such techniques are noninvasive and can readily be applied to humans.

That consciousness is a relatively high-level phenomenon has an obvious down side: it is likely incredibly complicated. We don't even understand how the motor cortex controls limb movement, a relatively simple phenomenon. It will take a herculean effort over many decades to develop the empirical infrastructure required to establish a consensus about how the brain is conscious.

In the next post, I'll switch voices and then we'll start in on ambiguous stimuli.