Some Thoughts on Information – V

(Click on a graphic to enlarge)

In this installment, I hope to cover how the information transferred from a photon to rhodopsin makes it to the brain. Visual information arrives at the retina of the eye as a spatial and temporal array of photons. In one sense, information is already digitized.

In Thoughts on Information III, we introduced the transduction of information from photons to G proteins. Let me just review that. Recall that the rod cell in the retina has the following structure:


If a photon of light activates the rhodopsin molecule, a G protein is generated. While it is possible that a single photon will activate a single molecule that will then generate a nerve impulse and pass the information up the chain to the brain (consider yourself in a pitch black cave; you might possibly be able to “see” one photon as a flash), in the more mundane case of day to day visual accrual of information, it probably takes many, many photons to cause a rod cell to fire. (if you are interested in the actual molecules involved, i.e. rhodopsin tranducin, please go here. http://en.wikipedia.org/wiki/Transducin

Recall that each of these reactions is catalyzed by an enzyme which is governed by the restrictions we discussed in Some Thoughts on Information IV.

That is, each chemical reaction is governed by the activation energy and statistics.

In summary, visual information arrives in the eye as a choreography of photons, a pattern if you will. This digital information (a photon is the ultimate in digital information) is transduced into G proteins. The G proteins cause a change in the sodium/potassium distribution across the rod cell membrane which creates an action potential in the axon of the rod cell.

Please go here for a dramatization of an action potential:
http://www.maxanim.com/biochemistry/Action%20Potential/Action%20Potential.htm



Please note that the action potential, just like the activation energy of a chemical reaction, has a threshold and that it is either generated or not. The action potential of any nerve is an either/or process. That is, again, it is digital information. This either/or process (no apologies to Kierkegaard) exists throughout the pathways and in the brain. Most importantly, because of this threshold, there is only one molecule difference between the non firing state and the firing state (action potential). Let me emphasize this:

In the generation of an action potential in the rod cells of the eye, it is the difference of a single molecule (e.g. G protein) which makes the difference between not firing and firing.

This action potential travels up the rod cell axon to the synapse with other cells in the outer layer of the retina as you will remember from the diagram presented before:



Please note that there are synapses at two layer in the retina before it leaves for the optic nerve.

Even in the retina of the eye there is manipulation of information. This manipulation of information is entirely understandable as basic electro chemical processes (action potentials, synapses, further action potentials) as we will discuss in a minute. It is highly likely that the basic scheme here is replicated in the brain in a much more complex way. But, the fact that information has pre analysis has got to be interesting.

One can assume that this processing of information in the retina served a purpose in evolution, perhaps streamlining the transmission to the brain. In addition, this just reinforces the observation that what the brain “sees” and what the eye “sees” are much different patterns. That is, the eye does not map the image onto the brain.

The transmission of the nerve impulse down the nerve is an electrochemical phenomena as previously described:
http://www.maxanim.com/biochemistry/Action%20Potential/Action%20Potential.htm

As each action potential reaches a synapse, the connection with the dendrite of the next nerve cell, there is a transfer of information across the space involving neurotransmitters.
http://highered.mcgraw-hill.com/olc/dl/120107/anim0015.swf

Once again let me emphasize that in order for the action potential to be produced in the second neuron, there has to be threshold reached, i.e. a certain concentration of sodium ions diffusing into the cell through the gated channels. Since there is a condition when there is no action potential and one where there is such a potential, there is the situation where one further ion of sodium is enough to reach the threshold.

When the nerve impulse leaves the retina, it travels via the optic tracts to the visual cortex in the occipital lobes of the brain.



There are many aspects of this information transfer that of interest both mechanically and from an evolutionary standpoint:

1. Because of the existence of neurotransmitters, one can assume that they were the way in which information was transferred in a primitive organism (this method is still used in humans in the endocrine system). It was only as the organism grew larger and became multicellular (there is a maximum size beyond which a cell will not economically function) that the evolution of nerves occurred. Still, instead of evolving a direct connection, organisms still retain the intermediary step of neurotransmitters. The system has to always be amenable to evolution even if it would be more efficient not to be. I suppose that survivability is superior to utility.

2. Previously, in Thoughts on Information IV, we suggested that one of the functions of enzymes was to bring the rates of biochemical reactions within the same time frame and that the overall rate was dependent on the slowest rate in the chain. In a similar way, the rate of information processing is dependent on the speed with which the organism can access information. This is, in part, dependent on the transfer rate of information. One can see that the simple diffusion of an informational molecule from a receptor to the brain would be far too slow to allow the organism to benefit from the information without the electrochemical conduction of the nerve. It is probably either the synthesis of neurotransmitters, or their release (a physical process that involves multiple steps) that is rate limiting in neurotransmission. All in turn are limited by the Arrhenius equation with the requirement that there be sufficient activation energy. (As an aside, in “The Stars My Destination” the hero gets a rewired nervous system. I assume that this involves getting rid of all those rate determining slow steps.)

3. Information transfer is quantized in that there is a threshold that has to be reached in order for the action potential to be generated either at the primary site (e.g. the eye) or in the transmission to the brain (at the multiple synapses). This threshold is dependent upon a single molecule. If the threshold is not reached there is no action potential. I feel strongly that this enormous implications for what transpires in the brain.

In summary, we have followed the quantized information in photons from the eye to the brain. We have observed that the electrochemical processes are governed by activation energy of enzymes but that the generation of an action potential is an either/or process. Finally, we have observed that there is preprocessing of information at the retinal level.

In the final installment, we hope to address information processing in the brain using the observations that we have made on the acquisition of information above.

Friday Crab Blogging (guest appearances)

No Crabs today; but, we had some unexpected visitors:

Including the Easter Hare:


Watering flowers

Standing on a Corner.....

(Firstly, let me apologize for the lack of posts. I am intent on finishing the thread on information and we're still sifting through the wreckage of our computer (Hal) crash of a month ago. I'm hoping to post again this weekend.)

The Growlery has a very interesting post up called Riding the (Carrier)Wave. He also has a second post since many, like ourselves, apparently found his discussion worthy of comment.

While there are a number of issues discussed there, it is the use of "quotes" from popular songs that most intrigued me. I suddenly realized where I had seen this before. Of course, it is scattered throughout Renaissance literature from Erasmus to Burton's Anatomy of Melancholy. The only difference is that the "quotes" here are from popular songs while there they are from classical tests, most often Horace, Cato, Cicero, etc. The author that quotes most deftly I find to be Montaigne. And, since he lets you into his personal life, it is pretty easy to see that his references are simply embedded in his life, just as popular songs are embedded in our lives, particularly from our youth. Or, as Montaigne himself says:

I quote others only in order the better to express myself.

The main difference is that when we write in blogs we can ever so easily crosslink.

So, "that will be the day" and "bye bye love." Or, my very favorite, since it evokes an entire era, "Standing on a corner in Winslow, Arizona,..." (Jackson Brown as covered by the Eagles.)

Friday Crab Blogging

No Snakes, No Crabs, but lots of rocks

Friday Crab Blogging

Friday Crab Blogging

From the Archives

The Libby Verdict

I really have to comment on the Libby verdict. Even though one of my friends feels that the moment of change was last November's elections, I really feel that this verdict, by a jury of randomly selected lay people, vetted by the defense attorneys, was a milestone. It was a demonstration that the American people, no matter what the World says about us, are, at heart, committed to the rule of Law. If only this could have happened before the tragedy of Iraq.

It is no matter that this will be overturned in appeal on a technicality. It is no matter that, if that fails, Bush will pardon little "Scooter" in January 2009. What matters is that, in spite of thousands of dollars on defense, the truth came through. That a Republican prosecuter actually achieved a conviction of one of the highest officials in the Bush White House. And that even at this date, the White House doesn't get it!

Comments on the Tangents

Our friend over at the Growlery has made some comments on our last installment concerning information. I realize that I am far behind in finishing up the bemusings, but really, HAL has been the most obstreperous of computers. He is quiescent now. Its hard to be your own I.T. tech.

Comments on the Tangents on the Comments:

Growlery: I would have been tempted to say that the brain is completely dependent, rather than "strongly dependent", on sensory information received. Even when surviving sensory deprivation, it falls back on recycling of external information previously received.

Dr.C: I would agree with this completely. Hopefully, when we get to the inner workings of the brain, this will be the crucial observation pertaining to free will.

Growlery:And I was amused by his use of the word "purpose" ("In spite of being in thrall to the imagination, I am sure you will agree that abstract creativity is not the primary purpose of the brain" - para 3, my emphasis). It is, of course, a figure of speech: I use it myself. My amusement derives from knowing that Dr C is usually more strict than I about not using language which imputes purpose to the products of blind evolutionary chance. Amusement aside, this says more about language, and thinking, and the symbolic bases of both, than about Dr C or myself.

Dr.C.: Again, I would agree that “purpose” is a loaded word. It is anthropomorphism at its sloppiest. I will be more careful in the future. Let us just say that although evolution is blind, it is also thoughtful. He (or She) would like to maximize a given species chances for survival (but not the collective species, i.e. life). Now this indeed is something to ponder. Talk about a tangent!

Growlery: Abstract creativity is the faculty which makes possible concrete problem solving in unexpected and unpredictable (even, on occasion, unimaginable) sets of new conditions or circumstances. It is at least arguable as a hypothesis that capacity for abstract creativity is the main factor in maximising the probability of survival, wellbeing and procreation for Homo sapiens. And if that hypothesis is accepted, then can it not be said that abstract creativity is the primary purpose (or at least a primary purpose) of the newest, most recently evolved regions of the brain?

Dr.C.: This, again, is just a rather heady grist for the ponder mill. One can easily see how the evolution of wings on a bird help it to fly. And then, the transformation of these wings to limbs (if I remember it right). But how does the ability to think (whatever that is) evolve? It must say something about the underlying structure of the brain. That is, the brain must be so structured as to allow evolution. So, I am going to store this question until we arrive at the brain itself. I only have a few things to tidy up on the periphery, but they are important.

Since Bill Evans on the piano is definitively abstract creativity. And there is many the man who seduced the girl (maximized his procreativity) using him as background, The Growlery has a point.

Friday Crab Blogging; From the Archives

Hope to get back to the board this weekend.

Occasional Turnoffs on the Freeway of Life

Not so fast, George!

Friday sort of Crab blogging

Some of us have imagination, some have artistic talent.

(And some of us have neither).

I apologize to any readers for the lack of posts. Our office computer HAL is having some problems and we are approaching Jupiter.

Friday Crab Blogging

Some Thoughts on Information - IV

Before we go any further, I wanted to point you to a collection of animations that are, in my humble opinion, superb in delineating the cellular processes that we are talking about. I will be using screen shots from these animations, and refer you to the particular animation in the future.

The animations can be found at: Max Animations

Review: We observed that the human brain is strongly dependent on information received through its senses. In spite of being in thrall to the imagination, I am sure you will agree that abstract creativity is not the primary purpose of the brain.

We have begun to follow information as collected by the eye on its path to the brain. To date, we have investigated the reception of a photon in the retina by rhodopsin in the rod cell, and have begun to examine the cascading pathway that will generate a nerve impulse. The next step is to view this as sequential chemical reactions. I promise that this is the lowest level (no quantum entanglement).

Axiom: In a series of chemical reactions, the overall reaction can only proceed at the rate of the slowest reaction in the series, i.e. the rate determining step. (I know this is obvious, but I really do think it is at the crux of many observations about information processing in the human.)

Observation: When I first started thinking about this I realized that any organism can be viewed in a number of “spaces.” The one that concerns us here is the kinetic space. The organism is a gigantic intersection of innumerable chemical reactions where almost all are catalyzed by enzymes. In other words, DNA, which determines the structure of enzymes, maps a metabolic profile onto kinetic space.

[A corollary of this observation is that the ultimate function of enzymes is to bring the kinetics of chemical reactions in the organism onto the same plane, i.e. within the appropriate time framework. All chemical reactions in the organism would eventually proceed in the absence of enzymes. Enzymes simply lower the activation energy of reactions so that they are time compatible. Otherwise, metabolism would only proceed at a snail’s pace, if at all.

What we are saying is that one part of evolution is changing the configuration of enzymes (proteins) by alteration of the DNA bases so that the rates of particular reactions (e.g. energy metabolism) are more efficient. In this sense, evolution is unidirectional and one cannot foretell what the upper limit will be. We can discuss the current limits though, see below.]

[Observation: Diseases such as cancer and the process of aging can be viewed in terms of kinetics. I have for some time felt that cancer is a kinetic disease. That is, that the basic biochemical defect (stemming from genetic defect) will be alteration of the kinetics of cell growth. This alteration not only produces abnormal cells, the cells themselves, of course, proliferate at a rapid rate (Burkitt’s lymphoma can double in 24 hours). Conversely, if cells in the blastocyst, which double in 12-24 hours, were allowed to grow without restriction, the blastocyst would soon be the size of a small universe. Evolution must have put into place a slowing of growth. Eventually, this would lead to the slowing of growth of the organism and, eventually, to programmed cell death (apoptosis).]

As we have stated before, all biological reactions are bi-molecular, and reversible.

A + B <=> C

Ah ha, you might say, isn’t an enzyme catalyzed reaction trimolecular?

A + B + enz <=> D

Well, I am almost certain that if the reaction time coordinate is divided into smaller and smaller intervals, you will always find that a substrate first binds to the enzyme then this complex reacts with the second reactant. The reason for this is simply statistics. A trimolecular reaction is vanishingly rare.

A + enz -> A-enz
A-enz + B -> D + enz

That is, the enzyme’s main purpose is to bring one reactant closer to the activation energy making it statistically much more likely that the reaction will proceed.

Here is an animation of an enzyme (I don't agree that both substrates bind at once).

This seems a good place to throw in my only equation so far, the Arrhenius equation:

k=A*exp(-Ea/R*T)

where k is the rate coefficient, A is a constant, Ea is the activation energy, R is the universal gas constant, and T is the temperature (in degrees Kelvin).

A schematic of how a bimolecular reaction proceeds is:



Now examine the Arrhenius equation. Please note that the higher the temperature, the larger the rate constant. This is one more clue that statistics are involved. Temperature simply increases the number of collisions that molecules have and their kinetic energy.

Consider the scenario: Many, many molecules are present in the interior of the cell. These molecules are constantly colliding with one another and with the enzymes (molecules) present. Many of the collisions do not result in a reaction of A + B -> C. It is only if the sum of both kinetic energies of the involved molecules equals the activation energy will the reaction proceed.

We have now gone to the very heart of the situation in an organism.

All metabolic processes, including the assimilation and transfer of information (such as the visual stimulus of a photon in the eye) ultimately depend on the bimolecular reaction of molecules which reaction is more or less statistically probable depending on the activation energy. Enzymes are no more than adjuncts to this by making the reactions compatible in a kinetic space.

[I cannot resist jumping ahead a little and asking you to please remember that this is purely statistical and mechanical phenomenon. If we were a Fermi genius and could track each and every molecule and its kinetic energy, metabolism would be entirely determinable.]

In the next installment, I hope to cover how the information transferred from a photon to rhodopisin makes it to the brain.

To be continued ………………

How can the obscene be beautiful?

This bomber has only one function in life, to destroy things and people. That includes children.

Is there any way out of the horror that we have created?

Who ISN'T involved?

McClellan - September 29, 2003: "The President has set high standards, the highest of standards for people in his administration. He's made it very clear to people in his administration that he expects them to adhere to the highest standards of conduct. If anyone in this administration was involved in it, they would no longer be in this administration. (emphasis added)"

Just substitute Iran

Letter to the Editor Re Iraq:
01/29/03 (Note Date)

I would have the people of the Eastern Shore consider the following:

There are 9,864,000 children in Iraq under the age of 15. These children are innocent of any crime. These children are in danger of being killed; nay, murdered. Already, sanctions against Iraq have caused an estimated 500,000 childhood deaths (~5%), the result of poor sanitation, disease and starvation. When even one child dies in our community, we grieve immensely. Consider yourself in the shoes of Iraqi parents who have lost their child to a cruise missle launched from hundreds of miles away. To them this is a weapon of mass destruction and, being human, they grieve.

I wanted to say that America has never been known as an aggressor nation; then I remembered what my brother told me about being in Vietnam. It was brutal. And I remembered the invasion of Cambodia in 1970.

As a nation we have power, immense power, but we are not using it wisely. Those of us over 50 remember when America was a good nation. We find that increasingly hard to say about ourselves now.

We must stop this impending war. There is no justification for it and it is clearly a grab for oil. The plans for its taking place were on the table before the dust of the World Trade Center settled. It will cause untold hardship for many millions of people, some of who may be Americans. It is not in keeping with our Constituion or our Spirit.

And it will result in the death of innocent children. Many, many children.

Friday Crab Blogging

Odds and Ends

The Growlery has directed us to a fascinating book review/commentary by Ray Kurzweil here.

The book reviewed is "The Intelligent Universe" by James Gardner; New Page Books, to be published February 2007.

Kurzweil points out that information technology has developed from carrying hand written letters by horse to the exponential growth of computing that we see today. His index is "computations per second," or CPS. The human brain is used as a standard (10**16 CPS). It is a relatively exciting journey through the future (we will apparently populate the solar system and then the universe with computation which is seen as a surrogate for intelligence, i.e. by 2029 computers will be powerful enough to simulate the human brain) winding up with some speculation about why we haven't found intelligent life in our universe (e.g. SETI and Fermi's famous question: "Where is everybody?").

Stanislas Lem has a rather bizarre take on this topic. In "Fiasco" he postulates that intelligent life has evolved many times in the universe but that there is a window of time that they pass through that is similar to where we are now and then they go to another level. We can't begin to even imagine the other level.

As usual, there is much to ponder in any missive on information. We were exploring it from a different perspective in previous posts. I think that we will come to some conclusions soon that might disagree with some of the more optimistic views of this review. This is because, just as with the constants in the universe and the speed of light (both covered in Kurzweil's review), the human mind has some built in limits related to biochemical rates. More on this later.

I was particularly struck by this quote:

“We have to regard these proposals to exceed or bypass the speed of light as speculative. But while this may be regarded as an interesting intellectual reflection today, it will be the primary issue confronting human civilization a century from now.”

One has to be very wary about predicting the future. Look how badly George W. Bush and Dick Cheney have done. However, this kind of "blue skying" has always been around since Plato down through Vico. Just in the last century or so we've had Jules Verne (who was frequently right on in many of his works) and H.G. Wells; Aldous Huxley (brave new world) and, ha ha, Woody Allen (sleeper). Multiple sci fi writers following the lead of Phillip K. Dick. Clarke in "Childhood's end" has the aliens being the devil with forked tails (explains a lot). I particularly like William Gibson with his gothic cyperpunk tales.

Another way of looking at the discussion of the universal constants (five) and how they have to be the values that we find to have a biological universe and life as we know it is to recognize that we find ourselves in the center of the universe in terms of scale. That is, going up by scale we approach the galaxies that comprise the known universe and down in scale to quarks. Why are we not closer to the upper limit than we are?

Of course Kurzweil proposes that some day we will at least occupy the entire universe with our knowledge/computation/whatever; and maybe even create new ones!!

Talk about intelligent (ha, ha) design.

Russ Feingold on Target

Game, Set, Match........

In the United States of America, the people are sovereign, not the president. It is Congress’ responsibility to challenge an administration that persists in a war that is misguided and that the nation opposes. We cannot simply wring our hands and complain about the administration’s policy. We cannot just pass resolutions saying “your policy is mistaken.” And we can’t stand idly by and tell ourselves that it’s the president’s job to fix the mess he made. It’s our job to fix the mess, too, and if we don’t do so we are abdicating our responsibilities.

Friday Crab Blogging

Handsome guy, wouldn't you agree?

Can you say obscene?

NEW YORK - Oil giant Exxon Mobil Corp. on Thursday posted the largest annual profit by a U.S. company — $39.5 billion — even as earnings for the last quarter of 2006 declined 4 percent.

A billion here, a billion there. Pretty soon....

From here:

The top five Gross Domestic Product (in billions of dollars):

Rank……Country………………..GDP
1…....United States.............$10,112.25
2…....China……………………….$6,716.20
3…....Japan……………………….$3,408.53
4……..India………………………..$2,808.83
5……..Germany………………….$2,126.60

Further down we have:
70.......Ecuador.....$42.27
71.......Ghana.......$41.96
72.......Croatia......$40.58

Exxon Mobile...........$39.50

73.......Libya........$39.04
74.......Slovenia......$36.72

In fact, Exxon Mobile made in PROFITS more than GDP of 108 out of the 183 countries in the world!

There are some very poor countries:

Country GDP/capita/year
Congo.........$883
Mali..........$877
Somalia.......$867
Nigeria.......$854
Niger.........$851
Yemen.........$831
Madagascar....$774

When you consider that:

In 2005, Lee R. Raymond (CEO of Exxon Mobile) raked in $48,922,808 in total compensation including stock option grants* from Exxon Mobil Corporation.

Which is at least $407 a minute, or about 1/2 the GDP per capita of someone in Nigeria, Yemen or Madagascar,

it makes you want to puke.

Some Thoughts on Information - III

This is taking a lot longer than I thought it would, and I'm still not to where I really want to be. So, tolerance, tolerance, please. Also, once into the nitty gritty here if I make a big boo-boo, please let me know.

I think we all agree that one of the most important events in life, maybe even the definition of sentience, is the reception, use, and ultimately dissemination of information (just gilding the lily on the dictionary definition of sentience.) So, the next thing to think about is how information gets to the human brain. Consider that, at the very root of this process, as, indeed the root of all biological processes, is a bimolecular chemical reaction. Hopefully, if I make it through this stage, that fact will lead to some interesting conclusions, if not many more questions, about information and its uses.

What follows is extremely simple at the basic level. The details (like the details of our discussion so far that seem to branch out further and further as the Mandelbrot set) become unbelievably complicated, e.g. the physics of photoisomerization. Please ignore the details if you wish. I will try to bring it to a very simple scheme at the end. Throughout, I have used Wikipedia. It is the current library of Alexandria.

First, consider a human who is in a tank of water that is at a temperature that is completely neutral (skin temperature). This person is able to breath with an apparatus and there is no light or sound. In other words, consider a person in an “Isolation Tank.” For short periods, this can lead to an enhanced state of self awareness, creativity, etc. However, after prolonged periods, the subject can experience anxiety, depression and, I suspect, just go crazy. (That sensory deprivation has been used routinely in the detention of “unlawful combatants” at Guantanamo and elsewhere is one more crime by the Bush administration, because it is certainly tantamount to torture.)

The point here is that the human brain has to have sensory input to function in a normal manner. In other words, it needs information. Without constant information input, the human brain and mind would go off on some wild tangent from reality. So, it makes a lot of sense to examine in detail how information gets to the brain and, by extension, how it is handled once there.

I would like to go through the process by which a visual sensory input (photons) makes it to the brain. Again, please try to see this in its simplest terms, since the devil is not in the details (except one, which I will come to).

It is of extreme interest that visual sensory input is quantized into photons. Please recall that Einstein won the Nobel Prize for this discovery, and the photoelectric effect, that he published in 1905 (along with the theory of special relativity!). While light behaves both as a wave and a particle (a photon), it is the latter that is of most interest here. In spite of this “quantization” it is my view that quantum mechanics plays no real part in the mechanism that we are about to discuss. We could talk about this at length later. Indeed, Einstein himself never really accepted quantum mechanics since it could not be brought into his general theory of relativity (i.e. couldn't explain gravity.)

I will try to show that at each stage of the process the information is digitized at the most basic level. This has profound implications for how we process the information and, ultimately must have some reflection on how we think. It also has a real world prediction about free will (don't choke, please).


Figure 1 - Structure the eye and retina


Figure 2 - Structure of the retina

First, consider the retina. It consists of multiple layers (see figures 1 and 2) with the rods and cones, the photon sensors, at the bottom of the layers (this is arrangement counter intuitive since you would think the photon receptors would be the first thing that a photon encountered). The rod cells of a human eye are capable of reacting to a single photon! That is, they are as sensitive as the Hubble Telescope since this is the ultimate limit of electromagnetic information.

In the cell membrane of a rod cell (cones are similar but are used for color perception) is a molecule called opsin (Figure 3).


Figure 3 - 3D structure of opsin

Buried in the center of opsin is a molecule called retinal (tiny red figure in Figure 3 and Figure 4 A). This is actually Vitamin A and, of course, the favorite of Bugs Bunny (carrots). It is also, sadly, very low in the diet of some third world children leading to blindness. We give it as a supplement to infants. Too much, though, is toxic. It is related to Retin A for acne, and, most interestingly, to the treatment of acute promyelocytic leukemia with all-trans -retinoic acid. How this causes differentiation of the leukemia cells to mature, non malignant cells probably involves G proteins, but I digress.


Figure 4A - Cis-retinal and 4B - Trans-retinal

When a photon of light hits retinal, it can be absorbed, causing the photoisomerization from the cis configuration to the trans configuration (Figure 4A -> 4B).

How exactly this is accomplished appears to be quite complicated. It can be understood in various ways. Since I am an aficionado of molecular orbital theory (vs valence bond theory) I prefer to think of it as the photon exciting an electron in the bonding orbitals of the retinal molecule to a higher orbital. Once in the higher orbital, the molecule is more stable in the trans configuration. However, if you are really interested, fly to here. This isomerization takes place pretty fast, somewhere on the order of 200-500 femtaseconds.

In the trans configuration, the retinal molecule doesn't “fit” into the opsin protein, and this causes a G protein signaling pathway to be activated. I am not sure of the exact mechanism of the pathway activation.

A nice animation of this process can be found here.

G proteins are ubiquitous in metabolism as “second messengers.”

The G protein in the rod cells is Transducin. Transducin contain both G-alpha and G-gamma-delta subunits. Activation of Transducin by the conformational change of retinal causes GDP (guanine diphosphate) to be exchanged with GTP (guanine triphosphate) from the cytosol at the G-alpha subunit. In turn, the now activated G-alpha subunit dissociates from the G-gamma-delta and increases the activity of cyclic GMP phosphodiesterase. This enzyme closes ion channels to passage of Na+ and K+ causing hyperpolarization of the cell membrane.



To be continued.....................

Odds and Ends

I am really working hard on the next "Information" post. I've gotten hung up on action potentials but, for anyone interested, I'll have it up later this week. I had to review such simple things as electrochemistry.

The Growlery has a couple of posts that bear commenting:

The source of the word "limey" is indeed from the practice of eating limes for vitamin C by the British Navy. I didn't mean it in a scurrilous tone by any stretch. While all the other sailors were getting the handle "scurvy bastard" attached to them, the Brits were drinking gin and tonic (quinine - malaria prophylaxis) with, of course, limes. There you are.

As for Pommie, I always heard it as "Pommie Bastard" when I lived in Ireland. But this was so long ago that it was at the beginning of the last "troubles" in North Ireland and it was used by the "Jackeenes" in Dublin. They're the ones who've lived in Dublin since before the Vikings got stomped by Brian Boru at Clontraf. I always thought was a reference to that little "pom" on the top of the British soldier's cap. I accept that it might have arisen in WWI with the influx in Europe of all those Australian troops fighting the "bloody Turks" and losing their legs as in "The Band Played Waltzing Matilda." Pomegranate sounds fine to me.

Aside stimulated by WWI and British soldiers: My college roomate's grandfather lived in Boston (on Beacon Street.) He was a doc in the British Army in WWI and had been in a mess tent in Egypt when T.E. Lawerence came rolling by. Small world.

Oh, about your Prince:

Prince Charles has been reminiscing about living in Australia as a teenager, saying he hiked for 70 miles and was called a "pommie bastard".

Here's another thing from the Growlery:

This question of symbols is one to which Jim Putnam periodically returns, for example here and more recently, less explicitly but just as certainly here ... it's a fascinating one, and goes to the very core of every area of human activity. Every one of us holds within her or his mind a model of the universe, and that model is built from symbols.

This whetted my appetite since there is no doubt that the internal workings of the mind must use symbols in some nuanced way and I don't, at the moment, have a biochemical explanation for this.

---------------

As for the comments by the Growlery re education and information, I wish I had an eon to reply. I can see I would have to sharpen the pencils since he has got the hands on experience.

Hat tip to Jim Putnam and his recent comments here. Again and again I go back to the scenario of "what should a good German have done." Norman Mailer's new book is about Hitler's early life; essentially an attempt to understand how someone could become such a monster. It may be that he was born that way, but certain experiences shaped him in his course. Are we not shaping the experience of children both in Iraq and, to a lesser degree in the West by perpetrating an endless civil war? What will be the result on the emerging Iraqi population? What will a young man of 5-10 years old be like in 15-20 years after having lived through this carnage. Has it not radicalized the Lebanese and Palestinians? Where does Ha mas and Hezbollah get its recruits except from this pool of radicalized young men, and, increasingly women?

We have much to ponder.

Friday Crab Rockfish Blogging

Slightly Limey?

Quick Comments

I feel very honored to have another blogger commenting on some of the things the Growlery and I have been throwing around. It just amazes me that the closer you look at even the most simple question the further it spreads out into even more interesting fields, like a Mandelbrot set. Take this remark:

In a previous life, my job was to assist clients to develop information systems. Reading Felix and Dr. C., I now become aware of how we limited our definition of information. Information, when designing a computer system, was data that was not previously known. In other words, our computer information systems allowed the manager to view data in such a way that some bit of data was used in a manner that allowed the manager to make better decisions.

Actually, I find this a provocative definition: "data that was not previously known." It casts information into a utilitarian role. Who would dispute that except perhaps an aesthete, i.e. one who valued information just for the sake of information. Perhaps an art connoisseur, or cellist. But then, you might rejoin that someone who just wanted pure information (if there is such a thing) was a dilettante.

You see what I mean, its like opening Pandora's box.

On another note, the Growlery has taken issue with my disparagement of Intelligent Design. That is a discussion that needs to be had, but I beg off until we get further into our current doings. However, I accept full sackcloth and ashes for belittling Intellectual Freedom even the slightest bit.

----------------

I suspect that we could go on talking about localization and dispersion of information for a long time and not even scratch the surface. It was interesting to follow the course from the Neanderthal, where almost all was localized in the individual, with some shared in the immediate community, to Homer where it was further dispersed, to the ages of libraries and print, and now to the age of the Internet. In each age the individual human has varying levels of on board information. As the Growlery points out, with A.I. robots coming on the scene, the delocalization of information is even more complicated.

But, we still have to get information into the human. From my standpoint, there are a number of interesting aspects of this process which we can go into in the next post.

Exactly how much information can someone know? How much should a person know (onboard v.s. access via, e.g., the Internet)? Is there a threshold amount of information after which the brain starts kicking things out the other end (wherever that is)? Furthermore, do we really forget things that we have learned or are they just non retrievable? Once you start asking these questions you can’t stop. Maybe I can make a stab at it after we develop information intake.

Aside: I am impressed that pedagogy spends little time teaching children facts anymore, at least as we were taught facts only 50 years ago, but I am not sure what is taught in its place. For instance, do they even teach the times tables anymore with the advent of hand held calculators? What about all those poems that people used to memorize. God forbid that I should ever have to go through medical school again (a recurring nightmare) and face that memorization gauntlet.

My staff, a number with children, informed me yesterday that they do not teach cursive handwriting anymore and that even in the early grades they learn keyboarding (which rhymes with skateboarding and, of course, snowboarding.) Children when they have to “write” by hand use printing. Sounds like regression to me. I suspect they will next be knocking out cuneiform script on clay tablets.

The Dying Children of Iraq

I promised not to blog on Iraq but I just can't stand this:

"Sick or injured children who could otherwise be treated by simple means are left to die in hundreds because they do not have access to basic medicines or other resources," the doctors say. "Children who have lost hands, feet and limbs are left without prostheses. Children with grave psychological distress are left untreated," they add.

They say babies are being ventilated with a plastic tube in their noses and dying for want of an oxygen mask, while other babies are dying because of the lack of a phial of vitamin K or sterile needles, all costing about 95p. Hospitals have little hope of stopping fatal infections spreading from baby to baby because of the lack of surgical gloves, which cost about 3.5p a pair. (emphasis added)

Yes, that's 3.5 pence, or 7 cents!

In the meantime, we are spending $2,000,000,000 a week killing Iraqis. The total cost of the Iraq "War" if over a Trillion dollars. Yes, that's $1,000,000,000,000. This would buy over 10,000,000,000,000 pairs of gloves. Ten trillion pair of gloves.

And I sit here doing nothing.

(Oh, and "Up to 260,000 children may have died since the 2003 invasion of Iraq." If America was Iraq, that would be over 3,000,000 children. That's three million. I can't even think about these numbers without getting ill.)

Some Thoughts on Information - II

We got as far as Homer with our thinking about information.

The reason I picked Homer is because, to my simple mind, he marks the transition for an oral tradition of information passage to a written version. When written language developed exactly is hard to determine (for interested parties, go to to the Wikipedia entry on the History of Writing).While there are surely sagas, stories, information (such as that found in the Egyptian pyramids) that had been written (using various hieroglyphic and cuneiform languages) prior to ~1200 BC, in the Western tradition, we credit Cadmus with bringing the Phoenician alphabet from Tyre (bombed to smithereens by the Israelis last summer) to Greece and introducing the written word there (as described in “The Marriage of Cadmus and Harmony” by Roberto Calasso.)

After this, information was written. At first cumbrous by hand, reaching its apogee in the scripting monks of the wee islands off the southern coast of Ireland (see “How the Irish Saved Civilization” by Thomas Cahill and, if you really want an experience, go see the Book of Kells at Trinity College in Dublin). This was a learning experience for humans, translating the spoken, observational world and mapping it onto the written page. This is the essence of writing, a mapping process. Interestingly enough, it is exactly what DNA does when it maps information onto the milieu of the cell. (To let you know where I am driving in these spiels, DNA maps its information onto proteins that have specific, kinetic rates. The proteins have primary (i.e. amino acid structure), secondary (i.e. how the amino acids are arranged determined by the code), tertiary (how the protein folds in three dimensional space) and quaternary (the rate of the reaction that the enzyme performs. Much more about this later, if you are interested, later.)

So information important to human survival is mapped onto the page by writing. Then, after Gutenberg, by printing. (Project Gutenberg is interesting in its quest to get as many books as possible onto the digital library of the Internet).And in the late 20th century by the digitization into ones and zeros.

This reminds me a little of the Jorge Luis Borges’ tale where the king asks his cartographer to map the kingdom and he makes a small model. Next he asks him to make it larger. If you know Borges, you can figure out what happens next. Gradually the map (model) gets bigger until it encompasses the whole kingdom. What I mean is that the Internet is digitizing our lives, at some point entirely. We don’t need to travel to distant stars. We can just send all the information necessary in digital form and another civilization will reconstruct us. DNA and all.

Now where is this information localized. Growlery emphasized that Homer’s information space was across Greece, several hundred kilometers. I would certainly agree with this but would also add that the next big thing after with written word was the localization of information in libraries, particularly the Library at Alexandria. It must certainly rank right up there with the seven tragedies of the ancient world the destruction of that library in that this was the largest collection of texts (many on papyrus) ever assembled until that time. It may have reached as many as 500,000 scrolls. (Laura Croft has an encounter with the Library in one of the Tomb Raider adventures, I forget which.)

As an aside, Egypt has recently decided to open a library to commemorate the ancient library. Do we not find an intense irony here that the written word is now digitized so that, rather than a library, we could store this on a few CD’s, or DVD’s, or Blue Rays, or whatever? (The library I now use is eMedicine, Google and Wikipedia, although I have a home library of 2-3,000 books. I just like to sit amongst them. Cheap thrills.)

So, back to the thread. In spite of the exponential increase in information, much of it localized in books, then books in libraries, one has to ask how the single human progressed in this. Did all this information make life easier for the human, or, paradoxically more difficult. And, of course, how do we get and process this information.

Stay tuned.

Friday Crab Blogging

An Oldie, but Goldie.

Further post on information this weekend, if anyone is interested.

Commenting before moving forward;

The Growlery has two posts up (here and here) with some pithy comments on what we discussed below. As I had suspected, there are large numbers of people who are thinking along the same lines, sort of like a “swarm.” Here are a few extracted memes:

Concerning Information handling in the human:

Now, though, I did think about it. And, she (his dentist talking about his tongue) pointed out, all of this is just one small subroutine within the total body monitoring run by the central nervous system - which is, in itself, only one function of that system amongst many others.

This comment is interesting from a number of points, not the least that it suggests that human processing of information is a massively parallel affair. This coincides with current ideas of neuroanatomy with the “executive” center being in the prefrontal cortex and the areas such as Brocca’s speech center (having been described several centuries ago) and the motor cortex being ancillary to this directive. Of course we don't really understand how it works yet.

Concerning Intelligent Design:

Human beings, as I said in an earlier post, are a package evolved by evolution (or, if you are from the other shop, designed) to meet a very different world from the one within which robotics are developing.

I disagree with the Growlery on tossing a bone to the intelligent design crowd. While they pretend to be scientists, their agenda is clearly political and it pains me that we have to continually recognize their influence. Hopefully it is waning.

Concerning Lagrange points L1 an L2
I looked them up in Wikipedia. It took me less than a minute. Talk about information handling.

Concerning deposits of information in robots:

...to duplicate them onboard is unnecessary, unless security or the transmission delay is unacceptable for a particular purpose

I think I would like to say something about this in the future. Something about the fragility of information transfer (upon which all these visions of robotic swarms heavily depend). Have you ever worked in a Hospital?

Concerning the robots of the future:

It's not impossible that dentistry, like radiography, will one day be carried out by machines; but not by a humanoid robot.

This is very poignant. It just like the American auto worker in the 50’s and 60’s looking forward to the future. Little did they know that their jobs would first be shipped over seas and then be taken over by automation. I don’t think that doctors (or lawyers, for that matter) have even considered what is going to happen to their professions when EMR’s (electronic medical records) get fully implemented. In fact, they are clamouring for my office to implement a prototype information collection on all patients with respect to their mental health that will be shared by all health care professionals!!

Talk about Brave New World (a Shakespeare quote, by the way. Never to be replaced by a robot.)

Concerning the definition of “living”:

When will a machine, robot, automaton, be deemed “alive”?

I would say that this is purely a philosophical question akin to “how many angels can dance on the head of a pin.” It is interesting if you read Wittgenstein to see how many of his “questions” about language are equally irrelevant a 100 years later. We should return to this after an appropriate science of neuro-informatics has been developed. Consider that working on these problems is just like Steven Weinberg and his theory of everything.

Next the Growlery refers us to five separate comments by Babbage and Lovelace. These appeared in 1998-1999 but are very relevant. The first of these is here:

What follows are just some quotes out of these commentaries that I found interesting:

Concerning “swarms” of automatons (I like this word in this context better than the word robot):

…It is not, he feels, a very great leap to imagine a linked ‘swarm’ of such vehicles, comprising, like ants, a greatly flexible, dispersed entity. The loss of a single automaton would not fatally injure the swarm, which could repair itself or even manufacture complete new vehicles. Perhaps such swarms are the future of planetary exploration and much else besides.

I think that this is a comment on the definition of life. What else is an organism but something that can “repair itself and manufacture copies of itself?” Of course that covers the Andromeda Strain and I despise Michael Critchon.

Returning to this question again:

Human sentience, it has been argued, derives from manipulative capacity and a critical number of neural connections. How large must a swarm be, Babbage wonders, to provide that critical number? He finds the question fascinating; but with the prospect of automata free to decide to copy themselves or to kill, Mary Shelley’s warning about irresponsible scientific creation carries as much weight today as it did when Babbage, as a young man, first read Frankenstein.

The Pope does Computers:

Lovelace turned to the radio, where she heard that the Vatican reputedly plans to computerise "the search for God's fingerprints in the chaos of Creation".

What an enticing little tidbit. Except, as they point out, how do you decide what is a fingerprint of God?

Dance, angels, dance on that pinhead.

On the fundamental constants of the universe:

that the fundamental constants of the universe - seemingly tailored to our existence - may also have evolved Darwinistical

I am not a physicist, but this seems to be contradicted by the fact that, as time goes on, we are able to reconstruct the universe further and further backwards in time. I am almost certain that this presupposes that the constants don’t change (wouldn't be a constant, would it). There is much speculation about these constants and, of course, the possibility of alternative universes comes up. It is my understanding that humans couldn't’t live in an alternative universe simply because only these constants only allow life as we know it.

Finally a comment on robotic surgery:

Of the medical endorobotics experts Babbage spoke to, some foresaw automated surgery useful in battlefield or other hazardous environments. Others saw brighter prospects, a way out of resource shortages in a world of escalating clinical demand. But whatever the applications for daVinci and the daVinciettes, their increasing part in medicine seems to Babbage inevitable.

Did I just see my job go down the drain? This is a long time in the future, but it is probably a real possibility. What will humans do when we are all replaced by robots. Oh, you Ludites, if you only knew!

Some Thoughts on Information

Some thoughts on the compartmentalization and dispersion of information in the biological world in response to questions posed by The Growlery.

This is such an interesting topic, and it ultimately reflects on the larger question of human knowledge, that it is certainly worth pursuing. Let me say from the outset that I am in no way an expert on these matters. I prefer to be viewed as a curious layman. And, I am sure, that people like Daniel Dennett have explored these issues far more deeply than I could even imagine (I have two of Dennett’s books and another on consciousness that I have yet to read). However, to just paraphrase what another writes, no matter how elevated, isn’t half as fun as thinking about it yourself. That’s why I like the Internet, it allows this kind of thing for a while (until the Korporate Takeover).

When was the first information necessary for an organism to survive? Well, it must have been pretty early in evolution that informational molecules were required. If we look on DNA as the current and ultimate repository of biological information, some prototype informational molecule must have been present from the word "go" to direct reproduction. If we had time travel, this is the first thing I would find out. What was the ur-molecule of life? Some have speculated that it was RNA, or an RNA precursor, but I think that unlikely. Even RNA, with its backbone of sugars, is much too complex. In any case, the necessity of information for survival dates from the beginning.

It goes without saying that this is what separates the animate from inanimate. There is no example that I know of where the inanimate is driven by information from another source. The crystallization of minerals into their complexity simply follows the second law of thermodynamics with the atoms settling into their respective potential wells in energy space. (This does mimic the organization of kinetic space in cellular metabolism but that is directed by DNA. More on this later.) In any case, the inanimate does not evolve.

Of course DNA and RNA are now the basis of all life, including pseudo life such as viruses. One has to wonder at how and why these molecules came to hold the position they do. In addition to being a very slick means of both reproducing and directing cellular events, the latter by taking information stored in the genetic code to direct the formation of proteins, these molecules are also easy to mutate. Without mutation, there would be no evolution. But mutation changes the information. Most mutations destroy information in that they direct the synthesis of dysfunctional or afunctional proteins. But some mutations, the saints among men, are actually “superior” or “new” proteins (and the use of the words “superior” and “new” here is very loose). They contain new information! (and “new” here is very tight). That is, the configuration of DNA base pairs is different, and this is new information. Of course, there is nothing new under the sun and some information has had to be “destroyed.” This raises the question if information can ever be destroyed. Once information has been present, even if the physical repository (here DNA) is it possible to destroy it forever? If the DNA for unicorns was once present (just like the DNA for DoDo birds and 99% of the other species that have ever existed including dinosaurs) does that mean that it never disappears, even if the information is not in real space? A mathematician must answer this question.

One should not dismiss lowly organisms such as bacteria from having sophisticated information handling (and needs). In addition to bacterial DNA (several have had their total sequence determined) there is bacterial phages, or viruses (virii?) that infect bacteria. In addition to being useful in the new science of gene therapy (getting DNA into human cells) they also carry information between bacteria in the process of infecting and destroying the bacteria (its every bug for themselves in the nether world.) This can be particularly nasty for humans because when a bacteria mutates its DNA to become resistant to an antibiotic, that new information can be relayed to all the other bacteria in the world in very short order by the intervention of bacteriophages. In this way, staphylococcus aureus has become resistant to almost all conventional antibiotics causing serious amounts of trouble treating infections with this common bug (the scourge of MRSA, of methicillin staph aureus).

Even inside the bacteria the information becomes more or less localized. However, it is not until prokaryotes evolve to eukaryotes, and we have a nucleus in the cell that we have true localization. At that point, we need messenger molecules to take the information out of the nucleus (messenger RNA) to the site of protein synthesis (ribosomes). Almost like a cellular internet.

In any case, while one is tempted to relegate “information” to higher organisms and even restrict it to humans, the reality is that all of life is based on information. However, as the Growlery points out, there is a hierarchy of information placement, though he restricts it to the human world:

… a tribal system of oral history and a Googlised internet are both points on the same continuum, albeit separated by an arc of accelerating complexity curve.

As organisms get more complex, information, information storage, and information access becomes more complex. At some point, information begins to be stored outside the organism. Now, to be sure, one can never separate an organism completely from its environment, everybody needs a Petri dish. We would have no viruses to taunt us if there had never been bacteria to harbor their growth. But we wouldn’t be able to eat steak either, since the intestinal flora help in digestion, including absorbing vitamins. What we mean here is that organisms extract information from the environment in order to exist, but I am not exactly sure how to say this. Is there a difference between my Googling “phage” on the Internet and a bacteria sucking up the phage du jour? This needs a lot more thought. What exactly do I mean by “extracting information from the environment” and how does this differ from just receiving sensory input. I know what I mean but I can’t express it. There is a difference.

Fast forward to mammals who walk upright. I have not read “The Singing Neanderthals: The Origins of Music, Language, Mind and Body” by William McNeill yet. I did read the NYRB review. It is an intriguing set of hypotheses but, ultimately, an exercise in metahistory. We cannot know what really went on in the camps of Neanderthals. However, it is a good bet that they did develop verbal communication. Most important here is that communicating by sound may have resulted in the establishment of a repository of information that, while not physically outside the individual, may be described as cultural or collective knowledge. Now, immediately you will put forward the objection that this is no different than the “instinctive” knowledge of bees in a hive or ants in a hill. Certainly those insects function with a certain amount of community information, and, they communicate. Ants with their pheromones and touch, bees with their visual dance.

But, somehow, once the Neanderthal started to collect information as language, I think we entered into a new era. You might disagree with me here. What we do know is that there were many thousands of years of oral tradition between the “Swinger” singers and the oral tradition of Homer. On the scale of true evolution, of course, it was miniscule (see the time line of evolution that was circulating on the Web in the last few years to counter the Biblical time frame.)

It is amazing, though, that Homer and the Neanderthals were both at the same level in terms of information. Of course aesthetically (a rather subjective thing) they are miles apart. It is interesting that the aesthetic appeal is due to complexity since there is no difference, basically in the level of information between apes singing around a fire and Greeks singing around a fire. This, of course, raises the question as to how complex the information can get? What is the upper limit? Is there always an upper limit and have humans reached the upper limit for our current brain?

So, next to take up information after Homer. It seems like the surface hasn’t even been scratched.

Bunnies

Tom Tomorrow's cartoon (which is always poignant) took a swipe at doctors today in the process of pointing out the absurdity of health care in the U.S. It makes me sad to see that someone as aware as he is about political events seems confused about what is going on in medicine. Doctor's have nothing to do with offering insurance, we only slave under it.

Dear Tom,

Doctors are not responsible and do not support the current fiasco that is health insurance. In fact, insurance companies are our bitterest enemy. They consume untold hours of staff time and pay only 50-70% of what they are billed. When is the last time you went to a gas station and paid 50% of what was on the pump?

Dr. C.

P.S. The CEO of United Health Care made $38 million in 2002.

Further Insanity

A U.S. attack plane killed many people with barrages of gunfire in a remote Somali village occupied by Islamists thought to be hiding at least one al Qaeda suspect, a Somali government source said on Tuesday.(emphasis added)

This is just wrong, wrong, wrong. Yes, there might have been an al Qaeda suspect. But there were innoncent people killed.

This makes it murder.

A small agenda

Being a little overwhelmed by the response over at The Growlery to a post I had below. Let me see if I can summarize the action in this flick to date:

1. Observation was made of the finding of random statue fragments (I almost said statutory) and the suggestion that information technology, if it can put together the Martian landscape, should be able to piece together the puzzle of a few dozen fragments. After all, a human can put together a 500 piece jigsaw puzzle pretty quickly and computers can beat the world champions in chess. I had been meaning to read The Growlery’s article on information processing and, indeed, he did reference this type of puzzle solving but then went on to mention some much more interesting things. I will switch from the terminology "knowledge" to "information" though they may be the same thing.

2. These interesting things included the fact that many organisms, including in large part human beings, must carry their information around with them (we all come with 10,000 genes for smell receptors; 10,000 pre programmed odors!!; gene knowledge and learned knowledge; classic platonic conundrum), that robots may be largely free of such restrictions. While the immediate needs of recognition may need to be on board the robot, a large amount of information in a robot may be stored off site. For example, as the Growlery points out, your personal robot might store your culinary preferences on the moon (as long, of course, as there was “instant” access through, I presume, a rapid satellite bluetooth connection.)

3. The first topic that we need to explore, then, is this idea of information localization. There are a number of fascinating aspects of this including Wikepedia, the fact that the Library of Congress could be put on a small number of CD’s, the emerging paradigm in medicine of information handling (are radiologists obsolete?) and, finally, the concept of human knowledge itself being located off site as in “cultural” or “tribal” knowledge. Pertaining to this the Growlery says:

Survival through all those millennia of pretechnological existence made us what we are: a fixed package of onboard facilities with expansion taken care of by social groupings.

Please take note of the social groupings, i.e. tribes. Is there dispersed knowledge a la Carl Jung? Of course humans now have Google which might make tribes, in the sense of Diamond’s progression of socialization (c.f. Guns, Germs and Steel) also obsolete, along with radiologists.

4. Once we come to some general conclusion about the localization of information (is not "knowledge" just "information" in context?) we need to address the actual procurement of knowledge by the human organism. On this, we will have to rely on some concepts of neurophysiology but will also need to extend it to the molecular level. This will involve a discussion of the “threshold” hypothesis of human action. I can’t wait.

5. With the tools developed in 4, then, and only then, can we address the concept of Free Will from a truly physiologic and molecular way. Even a causal survey of current human activity (particularly on a moral level) will show that if we come to the conclusion that humans do not have “Free Will” in any shape or form, then the entire society from top to bottom has to be rethought (including crime, including Saddam, etc., etc., etc.). Mighty big order, but even more interesting than 4.

Barbara Boxer the Ecumenicist

I was really struck by this:

Boxer said legislation on climate change will be her No. 1 priority as committee chairwoman. She plans to conduct hearings early next year with scientists, environmentalists and religious leaders who want to address climate change. She also will ask business leaders to testify about their efforts to limit greenhouse gases.

Religious leaders? What? Are we to include the local Swami? Maybe Pat Roberts and Billy Graham (though his kids are arguing about where he's going to be buried).

What does a religious leader have to say about the environment other than to take up our valuable public time arguing about intelligent design.

Geesh.

Bush and the Constitution

I just saw the video on Firedoglake of Olbermann talking to about the Constitution with a Professor of Constitution Law at GWU. Pretty sad. Pretty freightening. My reply.

The puzzles of Keros

Now here is a puzzle for any mathematician who reads this:

Statues offer clues to Greek isle's past
By NICHOLAS PAPHITIS, Associated Press Writer
Sun Dec 31, 4:19 AM ET

ATHENS, Greece - Unlike its larger, postcard-perfect neighbors in the Aegean Sea, Keros is a tiny rocky dump inhabited by a single goatherd. But the barren islet was of major importance to the mysterious Cycladic people, a sophisticated pre-Greek civilization with no written language that flourished 4,500 years ago and produced strikingly modern-looking artwork.
.................
...Keros is a repository of art from the seafaring culture whose flat-faced marble statues inspired the work of 20th century masters Pablo Picasso and Henry Moore.
..................
When they were unearthed, the white marble shards were jumbled close together like a pile of bleached bones, an elbow here, a leg there, occasionally a head. (emphasis added)

So, here's the challange, is there a program that solves a puzzle like this? That is, one that takes a jumbled mess of fragments and reconstructs entities? I would assume that there are puzzle solving programs just as I am sure that the topologists are all over this like chicken pox (ah, something I do know something about).



Oops, now that wrote all the above I see that Felix Grant has allready talked about the problem in his article on pattern recognition.

And, while I'm at it, let me throw out this quote from Dr. Grant's article:

..... a robot need only perform onboard perception and cognition where speed of response requires it – roughly the equivalent of instinctive functions in a biological organism.

It is my opinion, and I plan to spend a lot more time on this, that all functions of a biological organism are "instinctive." Actually, I would put the word "reflexive" there.

Furthermore, I contend that this includes all of the so called "higher" functions of humans up to and including Free Will. Take that you intelligent designers.

(Oh, and by the way, pattern recognition will be the death knell of radiologists.)

(And, of course, read Dr. Grant's article, it is very interesting in separating out the physical locale of knowledge. More on this and medicine later.)