Friday, April 27, 2007

Thursday, April 26, 2007

Storm Troopers of America

It is finally starting to sink into the thick skull of America that we have been led mightily astray by our President, his minions and the news media. Tom Shales yesterday in the WaPo about the Bill Moyers series on how the media mishandled the lead up to the invasion of Iraq:
Perhaps the truth shall eventually set you free, but first it might make you very, very depressed. Tonight's edition of "Bill Moyers Journal" on PBS is one of the most gripping and important pieces of broadcast journalism so far this year, but it's as disheartening as it is compelling.

It's always depressing to learn that you've been had, but incalculably more so when the deception has resulted in thousands of Americans dying in the Iraq war effort.
Yes, Mr. Shales, over three thousand Americans have died in Iraq. But, Hundreds of Thousands of Iraqi Citizens have died, many of them children!

Just look at this picture for a while. Imagine that it is your daughter humiliated by the presence of this sinister storm trooper. Your father has just been shot dead because he tried to defend his family by reaching into a cabinet for a gun. Yes, the trooper is an American. But this young girl is a human too. We have destroyed her life for now and the future. She no longer has an intact family. And all of this is so a bumbling idiot can "win" his "War."

I have no idea how Americans in the future, if we have a future, will be able to comprehend this.

Sunday, April 22, 2007

Reply to Comments

Jim Putnam and one of his commenters, Mac, were kind enough to offer comments on the last installment of the Information thread

Mr. Putnam states:
But I have a small point of disagreement:

What he describes here, in this specific essay, isn't information. It doesn't become information until it is recognized by the brain. It's merely a carrier, not matter how intricate or beautifully it has evolved to give us sight. ….. A map of that highway may be information, but the highway itself is not information.

Light wave/particles aren't information until they reach a means of converting and using them, in this case a brain. Until that point, it seems to me they're physical objects with no inherent informational qualities.
Later he says about recording thoughts:
…..The mind seems to conceive faster than words. I believe I think in words, in those cases where I actually do think as opposed to simply processing what's arriving through the senses, but recording thoughts is slow and laborious.
And Mac states:
While I'll admit to more than a bit of confusion on the subject, you (Putnam, drc) seem to be saying that 'information' comes into being only when acted on by the human brain. Although you do not use the term, it seems that to you, what exists prior to that human activity may be data, but is not information.
If nothing else, between you and Dr. C. there needs to be some agreement as to what this 'information' is that you are writing about.
Reply: Mr. Putnam’s point is entirely valid and it is a deficiency of my explanation that I did not make it more clear that what we were describing was only the manipulation and transfer of information from the perception in the eye to the brain. Please remember that this thread started from the observations of the Growlery about the evolution of robots and how they were not self contained but had to refer information back to the central processor and that this struck us as exactly what was happening in the human brain.

In the next installment, when we get information to the brain, I hope to discuss various ways in which the information can be recognized for what it is. At that point, we should commence a discussion of exactly what constitutes information as opposed to data. For the moment please accept my apology for being obscure.

The second blurb, on recording thoughts, I would also agree with. Many a time I have thought of something earth shaking to say in a post (or, at least, it seemed earth shaking at the time) only to get to the keyboard and find that it had floated off into the land where such thoughts go (imagine that country if you will; all the great ideas that were never recorded floating around like lost ghosts. A little spooky I would say.) As for the “speed of thought”, that is a very intriguing question. Because, much like a computer, the faster the thinking the more information that can be processed. This should be compared to the size of the brain. Of course this is similar to the clock speed of a computer and the built in RAM. It brings up questions as to why our brain doesn’t overheat when it is really thinking (yuk, yuk), or if that thinking is going on all the time, and how much is outside of "consciousness" (since Freud, there has been the idea that consciousness is only the tip of the iceberg. Some would say that all true decision making is below the surface and we only get the final “decision.” One can see that we need a new vocabulary to describe thinking since I hate putting words in quotes!)

In answer to Mac, we promise to try harder making distinctions.

We hope to have the final installment out in the next few days.

Friday, April 20, 2007

Friday Crab Blogging

This guy's been watching too many videos.

Sneaked a lobster in.

I know, Iknow. He's Sponge Bob's significant other. Whatever.

Tuesday, April 17, 2007


Condolences to the families and friends of the students and staff killed by the gunman in Blacksburg, VA.

Juan Cole has a very poignant post relating this to Iraq.

Saturday, April 14, 2007

Helpless in Never-Never Land

Since 9/11, when less than three thousand American civilians died in a suicide attack on the World Trade Center, George W. Bush has used this event relentlessly to press for endless war and the gradual destruction of our Constitution. He still apparently is able to obtain a response from Americans when he speaks (misspeaks would be a better characterization of his oratory) by repeating the mantra of "9/11, 9/11, 9/11." Now Rudy Giuliani, the then Mayor of New York City, is chanting this faux-religious chant in his attempts to gain the presidency.

While we have known how insane this is for some time, Americans are almost totally oblivious to the carnage that occurs on a regular basis in Iraq. This particular paragraph struck me in the "ho-hum" news piece that purported to report good news:
Figures compiled by the AP from Iraqi police reports show that 1,586 civilians were killed in Baghdad between the start of the offensive and Thursday.

That represents a sharp drop from the 2,871 civilians who died violently in the capital during the two months that preceded the security crackdown.
Do I need to remind myself and others that there is no difference between the people that died in the World Trade Center and the 4,457 that died in Iraq over four months? These are men, women and children, just like you and me, who have been caught in a situation of our making. They are, in a large part, innocent victims of civil strife generated by our presence there.

I feel absolutely helpless in the face of this horror. I was led to believe that voting for Democrats in the last election would change things. It has not. It is all smoke and mirrors and words. And there are no options except to see this played out over the years. Damn.

(Oh, and:
Outside the capital, 1,504 civilians were killed between Feb. 14 and Thursday, April 12 compared with 1,009 deaths during the two previous months, the AP figures show.

Friday, April 13, 2007

Friday Crab Blogging

Sort of an interesting critter. Claws define the Crab.

When you are really down, remember that children have the right view of the world. If I didn't know better, I would say this was Woodstock, 1968.

I apologize for not finishing the information thread, I hope to work on it this weekend. This is mainly because it inevitably has to leave the region of hard science. This includes answering the estimable Mr. Putnam concerning the medium and the message (Ah, Marshall McCluhan, you are so misunderstood).

Tuesday, April 10, 2007

How did we get here from there?

"Yes gentlemen, they are on their way in, and no one can bring them back. For the sake of our country, and our way of life, I suggest you get the rest of SAC in after them. Otherwise, we will be totally destroyed by Iranian retaliation. Uh, my boys will give you the best kind of start, 1400 megatons worth, and you sure as hell won't stop them now, uhuh. Uh, so let's get going, there's no other choice. God willing, we will prevail, in peace and freedom from fear, and in true health, through the purity and essence of our natural... fluids. God bless you all"...............

Friday, April 06, 2007

Friday Crab Blogging

Once again we feature a guest today, sort of an Alice in Wonderland theme:

It will be years before these two school girls, victims of a bombing last week in Iraq, will live in an environment where they can draw pictures like the above.

Thursday, April 05, 2007

Mr. McCain, please read this

This man has recently been in Iraq. He claimed before he went and while he was there that "things are going better." He visited a market (with a hundred troops, circling helicopters and wearing body armor) where he bought a rug.

Mr. McCain, your support for the occupatin of Iraq has led to incredible misery. Misery for which the world blames the United States, even though many of us have been against the invasion since its inception. If you doubt that there is misery, read this:

Sarah Abdullah, a beautiful girl of 8 years old, was an eyewitness to her father’s slaying two years ago, while he was giving her a lift to school one day in the predominantly Sunni Mosul.
Sarah, who could not speak for a while after the tragedy and who lost her mother from grief for her dead father, said “I knew that they went to heaven. However, I would look at the sky through my window everyday hoping to catch a glimpse of them.”

Ms. Khadija, the orphanage keeper or Mama Khadija as the children like to call her, told the independent news agency Voices of Iraq (VOI) “Sarah has passed through a difficult time. She used to scream at night and was unable to live with her relatives, but here she has found herself in harmony with other children.”
“She has been here for ten months now and still has nightmares. I stay up entire nights reading the Quran by her bed for tranquility. Sarah would sleep then as she embraces me,” the orphanage keeper said.

And this:
Hamid Abdul-Razzaq, 12, has sorrow stamped on his face as he lost his entire family when a mortar shell fell on their house three years ago. He was the only survivor because he was outside buying breakfast food for the family.

Hamid told VOI, “all words are in vain… I lost a whole family who were buried under my house. I cursed myself for not being among them when the round fell on them. What is the taste of life if you do not have a living father, a mother, sisters and brothers. Now I have none. The orphanage cares much for us but I would like to be part of a family rather than a member of an orphanage.”

Then look at these pictures:

Mr. McCain, what the United States has done, and what we are doing, in Iraq is wrong. Dead wrong. How can anyone be more explicit than that.

Tyger, Tyger Burning Bright….

Some comments over at the Growlery deserve some meandering in the blogsphere. First, the more one looks at the human eye (no pun intended) the more complex it gets. The eye may be the most sophisticated organ in the body including the brain. While we concentrated on the molecular events in the retina, maybe it is worthwhile to look at the overall structure for context:

From this site:
The retina is composed of 10 layers, from the outside (nearest the blood vessel enriched choroid) to the inside (nearest the gelatinous vitreous humor):

1. pigmented epithelium
2. photoreceptors; bacillary layer (outer and inner segments of cone and rod photoreceptors)
3. external (outer) limiting membrane
4. outer nuclear (cell bodies of cones and rods)
5. outer plexiform (cone and rod axons, horizontal cell dendrites, bipolar dendrites)
6. inner nuclear (nuclei of horizontal cells, bipolar cells, amacrine cells, and Müller cells)
7. inner plexiform (axons of bipolar cells and amacrine cells, dendrites of ganglion cells)
8. ganglion cells (nuclei of ganglion cells and displaced amacrine cells)
9. axons (nerve fibers from ganglion cells traversing the retina to leave the eye at the optic disk)
10. internal limiting membrane (separates the retina from the vitreous
We have focused on one of the sensing cells, the rod cells. The nerve cells that synapse with the rod cells and that we have assumed to have a “preprocessing” function would include the bipolar and ganglion cells:

Activated photoreceptors stimulate bipolar cells, which in turn stimulate ganglion cells. The impulses continue into the axons of the ganglion cells, through the optic nerve, and to the visual center at the back of the brain. There are about 120 to 130 million rods in each eye, and they are sensitive to dim light, to movement, and to shapes. There are about 6.5 to 7 million cones in each eye, and they are sensitive to bright light and to color.
This total to 130-140 million receptors!

From here:
There are approximately 1.1 million nerve cells in each optic nerve. The optic nerve, which acts like a cable connecting the eye with the brain, actually is more like brain tissue than it is nerve tissue.
Lets see: 130 million receptors funneled down to 1.1 million internet connections to the occipital cortex. 120 to 1. That’s a fair amount of processing in those bipolar and ganglion cells.

This just reemphasizes that information is preprocessed in the retina and that there is not a one to one mapping of image pixels (photons) to the brain.

And, you know, we haven't even touched on how or why evolution designed such a complex structure just to get the information from a few photons back to the brain. It is just amazing!


I had never thought much about “The Stars My Destination” since I read it in the late 50’s.

When it comes to pop culture, Alfred Bester (1913-1987) is something of an unsung hero. He wrote radio scripts, screenplays, and comic books (in which capacity he created the original Green Lantern Oath). But Bester is best known for his science-fiction novels, and The Stars My Destination may be his finest creation. First published in 1956 (as Tiger! Tiger!), the novel revolves around a hero named Gulliver Foyle, who teleports himself out of a tight spot and creates a great deal of consternation in the process. With its sly potshotting at corporate skullduggery, The Stars My Destination seems utterly contemporary, and has maintained its status as an underground classic for forty years. (Bester fans should also note that Vintage has reprinted The Demolished Man, which won the very first Hugo Award in 1953.)

Interestingly enough, I just read “The Demolished Man” and had no idea it was by the same author. I’m not sure how I got the name except that it might have been in a Wikepedia article on cyperpunk or something.

But, of course, “Tiger! Tiger!” caught my attention since a fragment of William Blake had come up when I Googled “Optic Nerve.”

Just go to Optic Nerve. There you will find this fragment of Blake's "Milton":
The Sons of Ozoth within the Optic Nerve stand fiery glowing.
And the number of his sons is eight millions & eight.
They give delights to the man unknown, artificial riches
They give to scorn, & their possessors to trouble & sorrow & care,
Shutting the sun, & moon, & stars, & trees, & clouds, & waters,
And hills out from the Optic Nerve & hardening it into a bone
Opake, and like the black pebble on the enraged beach,
While the poor indigent is like the diamond which, tho' cloth'd
In rugged covering in the mine, is open all within,
And in his hallow'd centre holds the heavens of bright eternity.

'Milton' - William Blake (1754-1827)

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Blake was not too far off if we assume he was talking about nerve fibers in the optic nerve when he mentions the Sons of Ozoth (don’t bother Googling "Sons of Ozoth", this guy only appears in Blake’s imagination; and doesn't his imagination sound like Lovecraft?) except 8 million vs 1 million is a little over the top.

But, back to “Milton” by Blake. This is one wild and crazy guy.

From here:

William Blake's "Milton" - Meaning and Madness

Most people know William Blake as the author of the poem The Tyger ("Tyger Tyger burning bright / In the forests of the night....") ……In his long narrative, "Milton", Blake describes how the author of "Paradise Lost" returned from heaven and entered Blake's foot in the form of a comet. Afterwards, the familiar world of the five senses turned into a shoe. Blake tied the shoe and walked with the Spirit of Poetry to the City of Art. A few years later, back in the ordinary world, Blake saw a twelve-year- old girl flying down to him. He mistook the girl for one of his own muses, and invited her into his cottage to visit with him and his wife, who could also see and hear "the spirits". The girl explained that she was actually looking for John Milton. The older poet emerged from Blake's foot, and in an apocalyptic scene, the ordinary world was transformed along with all of human perception.

Monday, April 02, 2007

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.

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:

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:

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.

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.