Wednesday, February 28, 2007

Friday, February 23, 2007

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, February 16, 2007

Tuesday, February 13, 2007

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:


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?

Monday, February 12, 2007

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)"

Sunday, February 11, 2007

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, February 09, 2007

Wednesday, February 07, 2007

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.

Saturday, February 03, 2007

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, February 02, 2007

Friday Crab Blogging

Handsome guy, wouldn't you agree?

Thursday, February 01, 2007

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):

1…....United States.............$10,112.25

Further down we have:

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


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

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.