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Tuesday, September 06, 2005

Evolution of sensory signaling

Echoed on the Panda's Thumb

How we sense the world has, ultimately, a cellular and molecular basis. We have these big brains that do amazingly sophisticated processing to interpret the flood of sensory information pouring in through our eyes, our skin, our ears, our noses…but when it gets right down to it, the proximate cause is the arrival of some chemical or mechanical or energetic stimulus at a cell, which then transforms the impact of the external world into ionic and electrical and chemical changes. This is a process called sensory signaling, or sensory signal transduction.

While we have multiple sensory modalities, with thousands of different specificities, many of them have a common core. We detect both light and odor (and our cells also sense neurotransmitters) with similar proteins: they use a family of G-protein-linked receptors. What that means is that the sensory stimulus is received by a receptor molecule specific for that stimulus, which then actives a G-protein on the intracellular side of the cell membrane, which in turn activates an effector enzyme that modifies the concentration of second messenger molecules in the cell. Receptors vary—you have a different receptor for each molecule you can smell. The effector enzymes vary—it can be adenylate cyclase, which changes the levels of cyclic AMP, or it can be phospholipase C, which generates other signalling molecules, DAG and IP3. The G-protein that links receptor and effector is the common element that unites a whole battery of senses. The evolutionary roots of our ability to see light and taste sugar are all tied together.

There's another class of senses that seem to function in a different way, and are distinct from the G-protein mediated senses like sight and smell. The G-protein senses are characterized by specific receptors tuned to recognize discrete elements—photons, chemicals, transmitters—in the environment. Sensing thirst, touch, vibration, texture, pressure, though, are different. There the stimulus is physical distortion, not a specific chemical agent. These senses don't use G-proteins, and are less well understood…but it's beginning to look like there are commonalities here, too, and we can trace our ability to hear and touch to a bacterium's ability to react to changes in salt concentrations.

What Kung proposes is that there are two very broad classes of primitive sensory signalling: one that detects solutes, molecules dissolved in the environment, which has diversified over evolutionary history to handle vision, smell, and taste; and another class that detects solvents, which has evolved to be used in our senses of hearing and equilibrium and touch. One way to think of it is that a bacterium's ability to sense when it is raining is the precursor to our ability to listen to music.

Here, for example, is a rod-shaped E. coli bacterium in an environment with some concentration of salts dissolved in it; it's in equilibrium. If it rains, though, turning our salty red world into a more dilute pink one, water flows into the bacterium, causing it to swell distressingly. The dangerous turgor pressure is detected by sensors that respond to the distortion of the membrane, opening pores large enough for internal solutes to flow out, restoring equilibrium and allowing the bacterium to relax back into its rod shape.

osmosensing
An E. coli cell in a normal environment (left) and in the rain (or upon dilution in the laboratory, right). A bacterium (shown as a rod), having adjusted its cytoplasm to the relatively high osmolarity of the surrounding milieu (shown in dark red, the red dots being solutes, not water), is confronted with a sudden dilution of its environment upon the onset of rain (light red). Entry of water (not shown) through the lipid bilayer swells the bacterium (now oval-shaped) and stretches open the MS channels to jettison solutes (red puffs), enabling it to reach a new equilibrium and escaping osmolysis (and returns to being rod-shaped).

So how do proteins detect the swelling of the cell? The answer is surprisingly direct: they have channels that respond to the tension in the cell membrane. Here, for example, is the MS (mechanosensitive) channel in E. coli. It contains a ring of helically organized rods that allow the channel to dilate open like the iris of a camera as the lipids in the membrane around it push and pull on its structure.

MscL
Helical segments (S1, S2, S3) and transmembrane helices (M1, M2) in one MscL subunit, as deduced from sequence and other analyses (left). Side (upper centre) and top (lower centre) views of the closed channel backbone structure of the E. coli MscL protein, by analogy to the crystal structure of the M. tuberculosis MscL homologue. The open structure deduced from both modelling and experimentation (right). Unlike MthK, the prokaryotic K+ channel that is equipped with a second constriction (the K+ filter), MscL is like the acetylcholine receptor/channel, in which the open gate doubles as the filter. Here the opening is huge (30 Å in diameter): befitting its ability to release solutes indiscriminately. The work to increase the area under tension constitutes the free energy difference that partitions the open and closed states.

These pores don't require any accessory proteins to do their job: they can be inserted into artificial lipid membranes, and they still function, responding to to distortion of the membrane by changing their permeability, which can be measured as a flow of current. Another interesting property is that they are sensitive to the lipid content of their surrounding membrane, which changes the forces exerted on them. Many anesthetics are readily dissolved in membrane lipids, and this may explain their mode of action—the E. coli MS channels can respond to exposure to procaine and tetracaine. That shot of painkiller you get at the dentist may work by making your nerve cell membranes more fluid and slippery, changing the way they can exert force on pain receptor channels.

We animals have other kinds of mechanoreceptors. Hair cells, indispensable for hearing and balance, rely on elaborate cilia coupled to TRP (transient receptor potential) channels in the membrane with tethers—tug on a hair, and it pulls or pushes on a structure imbedded in the membrane. The principle is the same, though, with tension between a protein and the lipids around it inducing a change in channel properties.

TRP sensors
TRP channels have been located in complex auditory sensory cells, even though the mechanism by which ciliary vibrations (arrow pairs) lead to the iris-like opening of the channels on the side of the cilia is not clear. a, The antennal chordotonal organ of Drosophila. CM, cap-cell matrix; DC, dendritic cap; CD, ciliary dilation. Red marks the location of NAN (a TRPV-type channel subunit encoded by the Nanchung gene). b, A vertebrate hair cell. St, stereocilia; K, kinocilium; PZ, pericuticular zone. Red marks the location of TRPA1. c, Models of the vertebrate hair-cell transduction channel. Molecular identifications have transformed the biophysical trapdoor model (left) to one with a TRPA channel and a stiff cadherin-containing tip link (right). The elastic element of transduction is now assigned to the ankyrin repeats in the four (presumably) TRPA subunits (shown as coils), which are presumed to be attached to cytoskeleton and/or myosin (not shown). This current model is compatible with one in which the displacement of the channel protein, with respect to the lipid bilayer, ultimately triggers the channel conformation change, right. However, none of these models should be taken literally since we do not yet know the true composition of the transduction channel(s) and how the various channel components contact each other and the lipids.

I'm feeling the keys under my fingers and seeing the screen in front of me and hearing the music on my headphones using a suite of tools derived from some primeval microbe's acquisition of sensors for dissolved nutrients and osmotic pressure. We've elaborated and refined and added new layers of complexity, but deep down we can still see echoes of our microscopic ancestors.

MscL
a, A diagram of an imaginary early cell equipped with two types of receptors that are required to sense solutes and solvents—the two ingredients of life's chemistry. The dots in the grey background represent water molecules (the solvent) and the red circles represent solutes (molecules dissolved in water). When a cell accumulates solutes, the internal water concentration is reduced and the tendency of water to enter the cell results in a turgor. Both the lock-and-key type of receptors (red) for different solutes (ligands), as well as the turgor sensors (blue) for water (the solvent), are needed for even an early cell to survive. b, A hypothetical diagram (not to be mistaken for phylogenetic trees) on the grouping of various senses that emphasizes the discrete separations of the lock-and-key type of sensing of the solutes (red) from the force-from-bilayer type of sensing of the solvent (blue).

Some people seem to think the linkage to our history demeaning, and take offense at being found similar to an ape. Personally, I find it uplifting and wonderful to see our unity with bacteria, fungi, worms, jellyfish, herps, and fish. What I love about biology is the way it binds us closer and closer to the world around us, and shows us over and over again that we're part of this place.


Kung C (2005) A possible unifying principle for mechanosensation. Nature 436:647-654.


Trackback url: http://pharyngula.org/index/trackback/2877/3VcOncXT/

Comments:
#39079: — 09/06  at  04:01 PM
Cool. I've often wondered how sensory perception is described by evolutionary theory. And I certainly agree with the sense of connection our common ancestry creates.



#39088: — 09/06  at  04:51 PM
That is quite beautiful.



#39095: — 09/06  at  05:22 PM
Great post!! The Kung article is very intruiging and I can't wait to see how some of the hypotheses play out. The TRPA1 KO mouse has to be close to arriving so it will be interesting to see what types of hearing and pain deficits the mouse will have. Another beautiful part of this story is the plethora of natural lipid products that have emerged to modulate these channels. From endogenous cannabinoids/vanilloids to natural products that we stir up in our kitchens, such as compounds in garlic, wasabi, capsaicin, cinnamon and the list goes on and on.



#39097: Mrs Tilton — 09/06  at  05:52 PM
Yowza! Excellent, interesting stuff.

And New Age 'synchronicity' into the bargain! For you see, I am working at the moment with a company that does interesting (and, for some unfortunate people, rather beneficial) things to G-protein coupled receptors. Not all that long ago, if you had said 'GPCR' to me, I'd have stared at you blankly. As I have since learned, they are the target of a huge percentage of all drugs.

If you are impressed by the sensory capabilities of human hair cells, BTW, we are going to have to have a chat about arachnid trichobothria.

You are right that people offended by our similarity to apes (sorry; I should have written 'to other apes') are stupid. But you do not go far enough. Our close connection to bacteria isn't merely wonderful and uplifting. It should also be a source of pride of the most snobbish sort: I will thank you to remember, sir, that my prokaryote ancestors were the first organisms to conquer this planet; and they dominate it to this day.



#39102: — 09/06  at  07:00 PM
This is interesting but it doesn't explain conscious experience. All this mechanical processing doesn't imply subjective experiences and could go on without them. An advanced anti-materialist but not anti-naturalist argument is presented in this article: Consciousness and its Place in Nature. Also, many of the explanations you detail are based on an outdated and false "Victorian" physical science. We're about 75 years into the modern theory of matter called Quantum Theory which isn't causally closed and provides bridge laws between mind-like aspects of reality and classical-physics-like aspects of reality. This book draft explains how modern physics relates to the brain and consciousness: The Mindful Universe (draft).



#39104: — 09/06  at  07:53 PM
I need to come back and read this when I'm not dead tired. It's very intriguing - I just blank out about halfway through a paragraph due to exhaustion. Maybe tomorrow.



#39105: — 09/06  at  07:55 PM
You should follow this up with a discussion of the neuroreceptors that actually process the data from the mechanoreceptors. If memory serves, aren't both types of senses processed by similar 5-HT receptors in the Raphe nuclei? I'm thinking specifically of how 5-HT2a agonist drugs can induce synaesthesia, but I'm sure there are other receptors involved. It might help your buddy Mark there understand the complexity involved in the sensory pathways that turn stimuli into electrochemical impulses, and then process and interpret those impulses.



#39110: — 09/06  at  09:10 PM
Mark, no one in their right mind would ever claim that the workings of the peripheral nervous system explains conscious experience.



's avatar #39111: PZ Myers — 09/06  at  09:17 PM
Uh, yeah, Mark...I don't know what you are talking about. This article is about sensory receptors, not consciousness.

But as far as consciousness goes, quantum babble explains nothing.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



Trackback: Making Sense of Senses Tracked on: PhaWRONGula (72.9.234.70) at 2005 09 07 02:00:57
Here lies essential unity, A carnal kin community, A bond of awed respect Wherein the feckless take offense...



#39122: — 09/07  at  02:41 AM
my favorite thing about sensory receptors is how they pop up where you least expect them...odorant receptors on sperm or axonal growth cones, for example. we think of senses in terms of consciousness, but all our cells need to sense things all the time.
speaking of consciousness...whoa...mark...dude. just because quantum mechanics is weird and consciousness is weird doesn't mean they're the same, or related. so many people get seduced by this...it made a quack of roger penrose with his undergraduate stoner microtubule theory and complete non-understanding of goedel's incompleteness theorem. as far as i know, there is exactly zero evidence that quantum effects have any bearing on neuronal function (and don't tell me that because a nerve firing is "probabilistic" it must be quantum, or isn't mechanistic. a coin toss is probabalistic but is completely mechanically determined by forces of my thumb, air resistance, etc).



#39125: — 09/07  at  04:05 AM
"This is interesting but it doesn't explain conscious experience. All this mechanical processing doesn't imply subjective experiences and could go on without them."

But the entirety of the mechanical processing in the brain *does* imply subjective experiences, in the same way that the entirety of mechanical processing in a healthy body implies good health. One could not have all the mechanical processing of a healthy body and yet have good health be missing. The idea that one could have all the mechanical processing of the brain and yet not have subjective experiences is a conceptual illusion. The philosophical zombie concept, which was invented by Robert Kirk as a challenge to physicalism, is actually a reductio ad adsurdum in favor of physicalism, which is one of the reasons that Kirk is now a physicalist (according to
http://www.nottingham.ac.uk/philosophy/staff/robert-kirk.htm,
"His book Zombies and Consciousness (Oxford: Clarendon Press, forthcoming) will to some extent atone for his error in having defended the possibility of zombies in articles in 1974").

To see the absurdity of zombies, consider that zombies are ex hypothesi identical in every detail to humans except that they aren't conscious. By this hypothesis, it is possible that every human being on the planet save yourself (assuming you know yourself to be conscious) is a zombie, including Robert Kirk, David Chalmers, and anyone else who has ever argued that consciousness is independent of the "mechanical processing" of the brain. In this view, everyone making claims about their subjective experience is making these claims for no reason at all; they aren't even lying, because lying involves conscious intent but they aren't conscious, being zombies. But this idea is as absurd, or more absurd, than the idea that genomes display hierarchical relationships for no reason at all. To the contrary, it is strictly the mechanical processes of the brain that result in the mental states of philosophers writing erroneous theses about about subjective experience being independent of those mechanical processes.



#39153: — 09/07  at  08:22 AM
The shorter answer to the zombie-phile is simply: "How do you know?"

I'm also fond of Paul Churchland's pointing out that the so-called impossibility argument rules out *any* explanation of consciousness whatsoever if it were successful.



#39189: Dennis — 09/07  at  11:54 AM
Did they do a homology search on these bacterial proteins? Specifically, did they find a homologous mechanosensitive channel in Arabidopsis? I did my Ph.D. research on mechanosensitive genes in Arapidopsis, and at the time I defended (only a little over a year ago) there were no candidates for a mechanosensory mechanism.

Crap, it looks like I'm going to have to subscribe to Nature just to read the article...



's avatar #39191: PZ Myers — 09/07  at  11:57 AM
They did mention homology between bacterial MS proteins and plant mechanoreceptors...

PZ Myers
Division of Science and Math
University of Minnesota, Morris



#39193: Dennis — 09/07  at  12:05 PM
(Cripes, one year and I'm already mistyping Arabidopsis...)

Now I definitely have to read that article... The research in my advisor's lab suggested a strong role for calmodulins and calmodulin-like proteins in transducing mechanical stimulus into a transcriptional response, which makes sense if you're opening an ion channel, but nobody had really posited any good candidates for a touch "receptor" at the time. I'll have to go and do a BLAST search for myself, and I'll definitely have to go back through my microarray data to check the expression of any homologous genes that turn up...



#39226: — 09/07  at  04:27 PM
"I'm also fond of Paul Churchland's pointing out that the so-called impossibility argument rules out *any* explanation of consciousness whatsoever if it were successful."

Indeed. Note that Chalmers' paper that Mark cites above offers this "argument" against materialism:

1) Physical accounts explain at most structure and function.

(2) Explaining structure and function does not suffice to explain consciousness; so



(3) No physical account can explain consciousness.

Sound familiar? Throw something about complexity into (2) and you get the intelligent design argument, but as written this is exactly the vitalist argument against explanations of life. Of course we know how that turned out in the informed scientific world, but there are still many vitalists among us -- in fact, I would say that the great majority of people are vitalists, and all of us lapse into vitalist thinking from time to time. But even if consciousness were different in this respect from life, (3) amounts to saying that it isn't possible to explain consciousness, because physical accounts are the only sort of valid explanations there are. Chalmers blathers on about "psycho-physical laws", but he might as well be talking of angelic-physical laws. Without a purely physical causal model, there's no reason for an intelligent informed person to take any claim about a psycho-physical law seriously. As you say, "How do you know"? Any so-called psycho-physical law could have the psycho aspect lopped off with Occam's Razor, with no damage to its accord with empirical observation.

The worst violation of Occam is this notion of quantum causal mind. Contra Mark, the reason that Libet's experiments showed that the action potentials in the brain that result in motor activity precede conscious decisions to engage in that motor activity is not to be found in supposed backward-in-time or faster-than-light implications of EPR, but in the simple fact that brain activity causes conscious decisions.



#39230: — 09/07  at  04:49 PM
I wrote "Contra Mark" -- oops, I thought this was Mark's book, and he sounded remarkably like he was channeling Henry Stapp. I didn't realize that it is Stapp's book. Well, that explains it. Stapp has been on this track for a long time, despite repeated refutations from both cognitive scientists and physicists.



's avatar #39430: — 09/09  at  11:55 AM
"as far as consciousness goes, quantum babble explains nothing."

Indeed! I would like to expand on PZ:s short description since this point keep resurfacing.

First, the arguments above are not decisive but shows clearly that the idea of a connection between quantum mechanics (QM) and consciousness is not needed.

Second, the proposition that QM is not 'casually closed', whatever that means, has probably its root in philosophical arguments with no concern for actual science. It is wrong.

In science causality means that you can predict a system's state from earlier states. QM is completely causal in that regard. In fact, since classical systems exhibit chaos (due to exponential divergencies that make pre- or postdiction difficult) but quantum systems still has not (due to linear divergencies), QM behaviour is easier to predict.

Third, there are several currently experimentally indistinguable interpretations of QM that leads to the same mechanics. (Someone refered to them as 'the faiths of QM'.) Some are unnatural ("anti-natural") and fall for Occam's razor. To the later group belong the interpretations that QM needs consciousness or many worlds to work.

While there are still some scientists that proposes some connection between consciousness and QM I think it is safe to say that it is now a crackpot theory.



#39532: — 09/10  at  04:24 PM
Hang on, Stapp seriously suggests that we have EPR bridges in the brain?

Now that is whacko, although it might serve to originate some more chat-up lines (along the lines of `come upstairs and see my wormholes').



#39604: — 09/11  at  10:09 PM
Not to disagree with folks about QM babble being useless to explain conciousness, but I would like to point out that currently there is conceptual difficulty in bridging QM states and probabilities with our experience of the classical world (where we feel things actually happen). There is also the question of free will. But this can't be solved by the likes of Penrose writing for the lay world with QM mumblejumble. It needs to be explored in the peer-reviewed science world first. However I don't think anyone is creative enough to come up with a convincing theory, yet.



's avatar #39750: — 09/13  at  06:28 AM
I disagree that there are conceptual difficulties to between QM and classical systems - but one has to give up some classical concepts when dealing with QM. Since QM is the more basic description the classical concepts does not apply outside the classical domain.

Free will can probably be substituted for consciousness in my earlier comment, except in the third argument. The conclusion will be the same: free will does not need QM and QM does not need free will. I think it is safe to say that to suggest connections between them are also crackpot theories.



#39954: — 09/14  at  01:30 AM
Hang on, Stapp seriously suggests that we have EPR bridges in the brain?


Libet's experiments appear to show that action potentials in the brain, which precede motor activity, also precede conscious decisions to engage in the motor activity. Of course these supposedly "counterintuitive" results are consistent with straightforward physicalism wherin conscious decisions are manifestations of unconscious brain activity but Stapp, who holds conscious thought and free will to be primary, needs some other way to explain the results, so he waves in the direction of EPR and backward causality (an incoherent notion if ever there was one).



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