SUPPORT DOCUMENT # 301

Plants and animals:

    In my theory I had suggested that plant and animals may be yet
another dichotomy based on energy moderation with plants at the low end
of energy moderation and animals at the high. It seems there is evidence
for that:

"The metabolic rate of most plant cells is well below that of the cells
of higher animals, hence their demand for oxygen and their production of
CO2 is much smaller .... plants, as a result of their lower metabolic
rate associated with a lesser degree of activity, tend to be without (a
special transport system) more often than animals ... Unlike plants,
animals are usually adapted for active locomotion. This means that their
metabolism is more rapid  ... In general, the movements and other
behavior patterns of animals are much faster than those of plants. Much
of the behavior of plants is dependent on variations in growth rates or
changes in the turgidity of cells, both of which are inherently rather
slow ways to bring about movement .... animals have evolved tissues etc.
... ;(On hormones) Given the inherent slowness of the mechanisms whereby
plants move the delay involved in chemical control is insignificant,...
slow chemical control is also sufficient for animals when instantaneous
response is not needed, as in control of digestion, salt and water
balance, metabolism, and growth. but when rapid response is required, as
in the movements produced by skeletal muscles, chemical control is not
sufficient. It is here that nervous control is essential."
Quotes from  Biological Science, William T. Keeton.

AND that nervous control  led to the evolution of brains in animals only.
They alone need them for quick response (and before that - for their
higher metabolic system)
Now we can look at plants and animals in a new way - as evolved opposite
ends of energy moderation

SUPPORT DOCUMENT #302

Repeat, repeat, repeat ...

    In my theory of health, I've developed a therapy that changes human
behavior by changing their subconsciously motivated system of energy
moderation. The system I use is a very very mild form of hypnosis in
that  it uses repetition to change the subconscious that directs most of
the physical body.

   It is interesting to note how most of the ways thinking animals learn
is through some form of repetition:

Habituation: which is a gradual decline in response to something
insignificant - learned through repetition.

Conditioning - the Pavlov dog salivating to the bell type response

Trial and error - if what it does works, it repeats it over and over.
What doesn't work it repeatedly does not do over and over.

Imprinting - does not seem like repetition but rather a short critical
period for learning - ex. in humans is language learning.

Insight learning - which isn't repetition, though it may have evolved
out of that (using past experiences to figure out new situations).

Repetition unlike psychotherapy, when done correctly,  works! And is
probably the only thing that does change
human behavior , safely.


I also think repetition works because it is a therapy that  seems to be
able to alter - at least somewhat - the behavior of the hypothalamus
which is the part of the brain that acts as the principal controller of
behavioral drives in higher vertebrates. It is interesting to note that
the hypothalamus contains the excitatory and inhibitory centers for the
various drives.
I would suggest that that is another dichotomy that has evolved out of
energy moderation with
excitatory drives probably coinciding with options 1 and 3
inhibitory drives probably coinciding with options 2 and 4

SUPPORT DOCUMENT #303

This and that

Here's some more comments on aspects of my theory.

"The development and maintenance of structures that no longer serve a
useful function would require energy that the organism might use to more
advantage in some other way."  (ex. given was eyes for cave dwellers)
This quote suggests that even loosing some aspect of an organism is a
form of energy moderation. It looses what it doesn't use, and frees up
more energy by doing so.

I have suggested that all life follows 3 modes of selection that
correspond to energy moderation.
1. Disruptive/scarcity , 2 Stabilizing (moderate amount of energy), and
3 Disruptive/abundance.
A great example of that are parasites. Parasites become more and more
selective. "Where an ancestral organism may have parasitize all species
in a particular family (which follows mode #1 scarcity - try anything)
each of its various descendants may parasitize only species in a
particular genus, or they may even be so specific that each can
parasitize only one species of host at each stage in its development.
(as the parasite becomes stabilized - mode #2, it begins to refine and
specialize)... Parasites often tend to become more specific not only
with regard to their host species but also with regard to the part of
the host's body they can inhabit... Internal parasites inhabiting the
digestive tract of their host are often restricted to one small section
of that tract." (Finally in an abundance of food/energy - mode #3, the
parasite can specialize to fit its specific wants. It also leads itself
into a corner (up an evolutionary creek) where it cannot change quickly
if something changes in its host. In essence we have a life history that
goes from hungry/will eat anything, to stable and has enough food, to
abundance and gets refined (and often extinct)

It is often stated that the cause of certain disease is that the
population that gets it has no defenses for the pathogen.
A common example is the Amerindians when subjected to diseases from the
invading Europeans. Yet if this was the entire story then the reverse
would be true as well. Just as the native population would have to form
resistances to the diseases of the invaders, the invaders would have to
form resistances to the diseases of the natives. And excluding some
sexually transmitted diseases, it didn't happen in reverse to the same
extent. This suggests that there is more to disease than pathogens. And
I would suggest that it is important who is conquered (overcome) and who
is conquering (overcoming) and that that is a factor of disease or
rather preventing disease. Though at this point that is no more than an
oversimplification.

Quotes from  Biological Science William T Keeton

SUPPORT DOCUMENT #304

Here's some more assorted comments on my theory of energy moderation

Even social behavior evolved out of energy moderation:

"... within a species there are two opposing sets of forces that
influence relationships between individuals - disruptive forces,
particularly competition, which tend to drive the individuals apart  -
in both the spatial and the evolutionary sense - (which would correspond
to options 2 and 4 - block out (move against) and excrete out  (separate
from))
and cohesive ones, particularly reproduction but often also increased
protection from predators and from destructive weather, which tend to
hold the individuals together."
(which would correspond to options 1 and 3 - take in (move towards) and
hold in (keep, conserve, hold)
The text goes on to list a number of ways the species does this -
spacing, clumping together ; territoriality and home range, social
hierarchies - pecking order, societies,  etc.  Also see how the 4
options correspond to the 3 inner conflicts in human behavior, as
written by Karen Horney in her classic book of psychotherapy, Inner
Conflicts.

I was stumped as to why any species when overcrowded would begin to slow
down reproduction. How did the group know to do that? One suggestion
that makes sense to me is this "there seems to be an endocrine feedback
mechanism that could help regulate and limit population size by altering
the reproductive rate. ..as the density rises and aggressive behavior
increases, endocrine disturbance rises and the reproductive rate falls;
conversely as the density and aggressive behavior decrease, the
reproductive rate rises."
(This also suggests that again energy moderation is the key . Aggressive
behavior is the clue - that evolved out of option 2 and 4 of energy
moderation.)

ATP is a key to energy for all life. Yet where did it enter history.
This text suggests "The two organic precursors of ATP are adenine, a
nitrogenous base, and ribose, a five-carbon sugar. Both of these
compounds also occur in nucleic acids, and experiments have demonstrated
that both can be synthesized abiotically under presumed prebiological
conditions." It seems that ATP was there at the start. (see my
suggestion that heat not chemical energy may have been the first use for
ATP)

Quotes from  Biological Science, William T Keeton.

SUPPORT DOCUMENT #305

Brain Research
In some recent posts people were talking about aspects of the brain.
Here's some interesting information.

Dr. Wilder Penfield has done some extraordinary experiments in brain
research. When Penfield stimulated certain regions of the cerebrum (the
big, multi folded top part of the brain) he caused some patients to
relive incredibly real memories.

The most interesting to me was one patient who, when a certain part was
stimulated , was positive
that the doctors were playing a record of a song in the operating room.
Her triggered memory was not a memory to her but so real she just knew a
phonograph was playing that song. And there are some other strange
points.

The memory played back in real time. If the stimulation is stopped and
then started up again, the song (or memory) does NOT begin where it left
off, but starts at the beginning - as does any triggered memory. And
finally the memories that are triggered are not - as one would think -
life shattering moments, but rather quite drab  but crystal clear
memories, that the patient seldom could recall without the stimulation.
"If these unimportant minutes of time were preserved in the ganglionic
recordings of these patients, why should it be thought that  any
experience in the stream of consciousness drops out of the ganglionic
record" Penfield

All this points to certain conclusions for me:
1. More memories are stored than we are consciously aware of
2. The stored memories can be played back (in stimulation at least), in
a way that makes them crystal clear,
3. These unconscious memories probably play a stronger role in our
behavior than we can imagine.
4. They probably play a part  in making dreams so vivid and real like.
5. The childhood memories that could not then be interpreted, probably
play a bigger role in our behavior.
6. The childhood memories that remain were made when the child was
unable to interpret their importance -
for example we learn how to turn off sensations that are unimportant at
the time - example when standing their is pressure on your feet, yet you
seldom think of it in the course of the day. Infants must learn all
this. So that at first they are bombarded with sensations that they must
learn to interpret.
7. Any therapy that would address human behavior or physical problems
would have to take the above in to account.

SUPPORT DOCUMENT #306

Plants & how sex may have begun

   The simpler plants seem to suggest how sex may have begun.
    In the Chlamydomonas  there are no separate male and female gametes.
Then in Pondorina there are 2 types of gametes with small male gametes
and larger female gametes with both still having flagella and free
swimming.
    In Eudorina the large female gametes are not released but remain in
the colony and are fertilized by the smaller free swimming male gametes.
In Pleodorina some of the female gametes lose their flagella and thus
become non motile egg cells. Only the male gamete is motile.

    What all this suggests to me is that the egg cells evolved into
those that stored the most energy, while the sperm cells evolved to
those that were the most sleek and quick. But this could be explained by
energy moderation. The egg cells could have stored more because they
metabolized less, with the most successful egg cells having the most in
reserve - unused. - ex. losing their flagella to conserve energy. While
the sperm cells used all their energy (and stored none) to sleek down
and become  more active with the most active impregnating the egg.
Thus sex is energy moderation.
(Facts here and below from Biological Science , William T. Keeton)
    *   *   *

It is interesting to note that the Paramecium has 2 different types of
nuclei
a Macronucleus and  one or more much smaller micronuclei.
The Macronucleus controls the normal metabolism of the cell while the
micronuclei are concerned only with reproduction.

To me this suggests the essence of life. One part metabolism (energy
moderation) and one part  replication  of that metabolism system (which
evolved out of energy moderation)
    *   *   *

The desire to stay alive EVOLVED and was most strong in those that
survived.  First life had no desire to live or die, or anything else
(including replicate or not replicate). First life just reacted to heat.
To suggest first life had any desires is to put human behavior on it.
    *   *   *
It is interesting to note that some blue-green algae (probably one of
the earliest life forms) have cells enclosed in layers of gelatinous
material. With the species occurring on wet rocks and other damp objects
where they form large masses of jelly.  This would suggest to me that
this jelly blob would protect most of the bacteria within it and could
be a highly protective development for the survival of blue-green algae.
It also suggests possible clues as to how life may have begun near the
shore (I have suggested tide pools) and may have  survived early harsh
conditions.
    *   *   *

SUPPORT DOCUMENT #307

Bacteria and Temperature - a mini version of my theory

    There is a chart of the growth rate of 4 types of bacteria at
different temperatures on the website

http://www.bact.wisc.edu/Bact303/NutritionandGrowth

This chart and the accompanying text  illustrates and sums up a mini
version of my theory

"Most bacteria will grow over a temp. range of 30 degrees. There is a
steady increase in growth rate between the minimum and optimum temps.
But slightly past the optimum a critical thermolabile cellular event
occurs and the growth rate plunges rapidly as the maximum T is
approached."

No matter the species of bacteria their growth/temp chart is exactly the
same a lopsided bell curve with a gradual slide up then a fast fall down
as temp increases.

Here is how this illustrates my hypothesis:

All life slows down in low temperature/energy and becomes more and more
active in high and grows  accordingly

In  too low energy, life slows down  and waits to be energized - then
begins to speed up again.
In too high energy, the DNA denatures and the organism dies.

Thus life - (that at this stage can be defined as chemicals in water
reacting to hot/cold cycles in nature) to sustain itself must find
strategies only for one of the 2 extremes -  for the too HIGH
energy/temp. It must find away to inhibit denaturing of nucleotides.
One of those strategies evolved to replication.

Inhibiting the denaturing of RNA or more likely GC nucleotide bonds that
preceded a RNA world,  (though it is DNA in the above chart) was
probably the key to life. From then on all life  - like all bacteria -
slows down in low energy and waits it out,  or some other evolutionary
strategy (store energy, find alt sources of energy , etc.)  and becomes
more and more active in high - up to the dangerous point where natural
selection only allowed those that could inhibit high melting T.  to live
on.

This is so clear to me. How can readers NOT see this? How can there be
anything but energy as the force behind life?
It is the 1000 pound gorilla in the room!

SUPPORT DOCUMENT #308

1st, 2nd, 3rd codon positions in thermophiles

I've suggested that a GC world may have preceded the RNA world that
led to first life.

    In looking at this website:
http://www.kazusa.or.jp/codon/

    I found some very interesting clues about first life. IF the
environment was very hot - and I think it was, and IF bacteria and
archaebacteria that live today in extremely hot environments, have
genomes similar to first life that had to survive that very hot
environment, THEN it would be interesting to find any patterns in the
codon structure of these heat lovers:
I looked at 7 -  such as pyrodictium aby SST, Pyrodictium occultum,
Thermococcus sp, etc.
and they ALL had the same pattern in 2 instances - more so in point #2.

1. a high G-C content (the 3 hydro bonds of GC melt slower than the two
of AT -  (AU in RNA - which I am interested in when it comes to first
life)

But even more impressive is the GC placement in the  3 place codons:

2. the same pattern of high GC in first place, low GC in second (thus a
High AT) and a high GC in 3rd place.

Why would ALL of these heat lover bacteria have G or C on the ends? IMO
it is clear that it is because
THEY MELT/DENATURE AT A HIGHER TEMP.  then the AT.

Therefore it would suggest to me that in first life my GC world would
begin to accept AU nucleotides (this is RNA now with U replacing T)
only in the protected center position, because the heat/cold cycle was
such that only GC bonds could survive denaturing (and probably only
after they had grown to some complexity or longer strands). Thus the
only amino acids that would survive are those of ALL 3 positions filled
by G and/or C OR the ends filled by G and/or C but the interior position

could now be filled with A and/or U.

Some feedback:
The second codon is the most highly constrained. A change in the
> second position always results in an amino acid replacement. It would
> be least subject to AT or GC mutational pressure. This position
> therefor has the narrowest range, maybe a range 35% to 42% when
> looking at both high G-C and low G-C organisms. But you are correct
> that it always has a low GC content.
>

> The first codon is constrained but not completely. UUR and CUR (both
> Leu) and CGR and AGR (both Arg) differ only in the first codon. As
> expected, the first position has a wider range, maybe 42% to 65%. You
> are correct that it always has a higher CG content that the 2nd
> postion.
>
> The third position is minimally constrained. In many cases the first
> two postions determine the amino acid and it doesn't matter what is in
> this position. In a general sense, this third position will approach
> the CG content seen in the unconstrained spacer regions. In high C-G
> organisms this third position will be very high. In low C-G organisms
> it will be very low. For example, compare the third position in
> Mycoplasma capricolum (about 25% genomic C-G) with Micrococcus luteus
> (about 75% genomic C-G).

> William L Hunt


SUPPORT DOCUMENT #309

2 more points on my hypothesis:

1. On primordial soup:
"Neither oxidation (there was no free oxygen) nor decay (there were no
bacteria) would have destroyed these (primordial soup) molecules, and
they would have accumulated in the oceans for hundreds of millions of
years. With the accumulation of these small organic compounds, the
oceans became a thick, warm organic soup containing a variety of organic
molecules."  Biology, Sylvia S. Mader

This suggests a great kettle of ingredients all ready to come together
and plenty of time to do it in on early earth.

2. First cell idea

Also IF my idea of a GC world is correct and it led to the first RNA as
protein maker, THEN wouldn't it be possible for RNA to begin making
protein (and as enzyme  and replicator too), and wouldn't that new
protein be clumped around the RNA, and wouldn't  you ,at some point,
have a ball of protein surrounding that RNA, and isn't it possible that
lipids could form around the ball of protein around the RNA?

And finally, albeit very very very small - wouldn't you have a cell -
with a protein and fat, membrane and RNA inside of it. And then couldn't
the cell over billions of years grow larger to the maximum size allowed
by surface area to inside volume like we find today?

SUPPORT DOCUMENT #310

Building on Darwin's discovery

My hypothesis enhances Darwin's work in 2 areas:
One it explains a possible 'how and why' life began as energy moderation
And  two, IF that is true it sets up a way to alter human behavior for
the better by altering that
energy moderation system. Plus a therapy to do just that.

(Actually the hypothesis was worked out backwards - from human behavior
back - that's why the
akward biological info on some of my earlier  posts)

Everything I've said is built on the work that has gone before me. If I
am correct, it is because
I've expanded on those ideas. Note that wherever possible I'll quote
text to support my ideas.

The major difference in my theory and the work of others is the emphasis
on metabolism over replication. 

SUPPORT DOCUMENT #311

Proteins and enzymes denature and anneal too

    In my hypothesis I suggested that life may have begun in an GC world
that preceded an RNA world. The process was simple. The primordial soup
of nucleotides would follow the heat/cold cycle on the earth. Those that
led to life - specifically GC - were best suited under the temperatures
of early earth to both denature and anneal under those temperature
conditions.

    This same process works not only in denaturing and annealing
nucleotides, but also the much more complex proteins and enzymes.
Let's say that my suggestion works and the nucleotide strands (mostly
GC) begin to build complexity. At some point there should be formed
proteins. But proteins denature and reactivate too. "When a protein is
denatured, it loses its normal shape and activity. IF denaturation is
gentle and if the conditions are removed, some proteins regain their
normal shape. This shows that the normal conformation of the molecule is
due to the various interactions among a set sequence of amino acids."
Biology S. Mader.

   This suggests that the same heat/cold cycle that built up nucleotides
could possibly be a source of variety in coding proteins and enzymes.

    *   *   *

    In a previous post I suggested that the growth/temp. chart of varied
types of bacteria  summarized many aspects of my hypothesis.  The chart
for the rate of an enzymatic reaction as a function of temperature - is
also the very same shape. A slow slope up to the peak, then a quick
fall. Specifically in an ex. given in the text cited above "at first, as
with most chemical reactions, the rate of enzymatic reaction doubles
with every 10C rise in temp. The rate or reaction is maximum at about
40C then it decreases until the reaction stops altogether, indicating
that the enzyme is denatured."

    *   *   *

    I tend to think that this lopsided bell chart is a key to all life
in that it charts  growth ,metabolism, etc. as an aspect of
temperature/energy. All life slows down in low temperature/energy and
speeds up in high. But too high and life functions stop. Thus the key to
first life was inhibiting this 'too high' temp.  Slow slope up the
curve, peak, sharp cliff down.

SUPPORT DOCUMENT #312

Life at High Temperatures - quicker replication, etc.

Here's a fascinating net article on "Life at High Temperatures",
Thomas A Brock

http://www.bact.wisc.edu/Bact303/b1

There were certain parts that IMO gave clues to first life:

"In addition to living in boiling water, these prokaryotes are growing
surprisingly rapidly, a population can double in as few as 2 hours ..."
(also)
"Algae, bacteria, and invertebrates all grow faster and to higher
numbers in the heated portions of the river."

These 2 quotes suggest to me that temperature and replication rates may
be connected. In my theory I suggest that very thing. Specifically that
replication of cells began as partly a way for the 1st cell to survive
high temperatures - thus the hotter it would get the more it would have
to shed off as waste - which later evolved to half of self out as waste
which evolved to  binary fission. A cell too large outgrows its outside
skin to inside volume ratio and cannot survive. Replication resolves
that problem by cutting the cell size in half and allowing it to
continue to exist.

Also these springs supply minerals to these prokaryotes, "The water of
Yellowstone's thermal features is not only hot but mineralized ...
minerals provide the nutrients that feed the microorganisms." This would
suggest that in early earth, some volcanic activity could be
advantageous to first life, in that it brought up to the surface - like
Yellowstone hot springs - a continual supply of needed minerals etc.

The report also notes that there are dozens of bacteria life at this
high temp ( I tend to think this is similar to the temperature that life
began at); and it notes  that some prokaryotes can survive temps of 115
C.

And finally that in some of these heat lovers, there is a very high GC
content - which I suggested is a key aspect of the pre RNA world of
first life:
ex. include :
Thermus aquaticus with  the following average codon positions :
1 position -  68% GC, 2 - 42% (the protected position), 3 -  89%  GC
Thermus caldophilus
 GC  1 - 70%, 2 - 42%, 3 - 92%

SUPPORT DOCUMENT #313

"Look Humans, No Hands, click click"

    The usual arguments for brain development in humans often includes
the following:

Stereo eyes moved to the front of the skull, wide upper arm movement to
swing from trees, a hand to grasp the branches with that  all important
thumb, then down from the trees - bipedal motion  ( Sylvia Mader text on
Biology suggests that humans separated from apes as  the north-south
running rift valley in eastern Africa began to separate eastern Africa
from the rest of the continent - tree livers on the west side, grassland
survivors - hominoids on the east) and finally that hand to make tools
while walking.

It all sounds wonderfully logical until you suggest that DOLPHINS are
arguably the 2nd smartest and largest brain species and they  did NONE
of the things suggested above for hominids. So how did dolphins get so
smart without tree training, bipedal walking, etc.?

I welcome all comments and give a few of my own here:

Though all the things above probably contributed to intelligence, I
think the key to brain development can be found in those aspects that
Dolphins and Humans have in common.

This site is a fun and informative intro to the bottleneck dolphin
http://www.seaworld.org/bottlenose_dolphin/

There are some points in these pages that stood out for me and my
theory:
They are mammals too, they sleep 33% of the day, they have a high
metabolic rate - higher than land animals the same size, with a
temperature of 36.9 (humans at about 37), and high sense organs of
hearing and sight, plus

"Field observation suggest that mother - calf bonds are long lasting...
A  calf typically stays with its mother 3 - 6 years or more. ...Adult
male pair bonds are strong and long lasting. Male pairs often engage in
a number of cooperative behaviors... Social behavior comprises a major
portion of bottlenose dolphins daily activities. Also it said that often
dolphins giving birth will have a 'nanny' dolphin  nearby to help in any
way it can. And that  the mother passes considerable amounts of
information to the calf.
All this strongly supports the mother/child bond and the strong social
behavior among dolphins.

In my theory I have suggested a key to brain development is the mother
child bond, something I call "Carrying the baby"
Yet how could this be in dolphins with flippers? " The baby swims close
to its mother and is carried in the mother's 'slipstream'. The
hydrodynamic wake that develops as the mother swims. This helps the baby
to swim and enables the mother and calf to stay up with the group...."
(Dolphins version of carrying the baby?)

So in summary these are the factors that both species share and that IMO
may have helped brain develop to such a high degree :

Carrying the baby - the mother child bond (note how much we humans wish
to please our mothers by learning a lot and quickly) PLUS perhaps the
main key - a protracted learning period in calves, children.
Social behavior
Language - though no real language among dolphins there are whistles and
clicks and hearing is highly evolved.
Age - dolphins live  about 20 years (some as high as 48). For comparison
just imagine human culture void of all discoveries and innovations made
by humans past the age of 20!
A large brain needed to run a high, warm-blooded metabolism
Size - Large animals needed to house a large brain

SUPPORT DOCUMENT #314

"Look Dolphins, no flippers." Or
Helplessness Helps Humans

In reading a recent text on brain development, I found some passages
I strongly disagree with:
Biology, S. Mader is talking about human brain development - with a
research report by Steven Stanley, The Johns Hopkins U.

"Unlike other primates we retain the high rate of fetal brain growth
through the first year after birth."
OK so far.
"Although the human brain becomes much larger, human babies are
remarkably weak and uncoordinated. Such helpless infants must be carried
about and tended. Human babies are unable to cling to their mothers the
way chimpanzee enables can."
OK still.
"...at the time the Homo genus evolved, the climate was becoming cooler
and drier. This caused forest to shrink and grasslands to expand across
broad areas of Africa."
OK
"Humans gained a large brain, but they were saddled with the largest
interval of infantile helplessness in the entire class Mammalia. The
POSITIVE VALUE OF A LARGE BRAIN MUST HAVE OUTWEIGHED THE NEGATIVE
ASPECTS OF INFANTILE HELPLESSNESS ,... or natural selection would not
have produced the Homo genus.

This is a case of the background information being correct but IMO the
interpretation of that info incorrect.
What I suggest is that  the  so called "negative aspects of infantile
helplessness"  were not negative, but the positive reason for brain
development - just the opposite of what he suggested.

The long nurturing period of human children  - far from being a negative
aspect - is the most positive aspect of brain development in that it
allows the child time to learn from his mother  and develop a strong
mother-child bond that  gives strong incentives for  more learning and
stronger social ties. Humans WANT to please our parents. And what the
human species has done is reduce instinct learning (born into the child)
and even most  imprinted behavior for learned behavior.
And replaced it with learned behavior - or cultural learning.

It is difficult for science to treat love as an evolutionary step. Yet
in my theory it is a part of energy moderation that evolved to symbiosis
that evolved to love etc. And the mother/child bond is the main version
of this love. It isn't just nice and pleasant - it is the key to most
brain development in humans.

The author then goes on  to say it'll be a great discovery to find the
mutation of a regulatory gene that could have delayed early maturation.
Yet natural selection would do that with more needy babies requiring
more love and attention and in return developing stronger brain
development ,as well as stronger love bonds with the mother and tribe
that raised them).

SUPPORT DOCUMENT #315

Reply to my post on the GC world by William L. Hunt

I previously posted saying you were off target with your arguments.
 Because of your strong belief in the importance of GC, I pondered
whether there could be any logical connection between the GC bond and
the universal genetic code. I saw a connection and the post argues the
connection.
  I don't generally hold your views. I haven't read your Theory posts
in a long time, but I think I'm arguing for your case by the end of my
post. I just followed my logic whereever it pointed.
 I am a computer programmer and not biologist or biochemist. I am
comfortable with encryption systems, encoding and decoding systems and
how such systems can and do handle errors. I am not comfortable with
biochemisty. I look at the universal genetic code from this direction,
and not from the details of the biochemistry.
 This is a long note and a long post but you may find it interesting.
  William L Hunt 
--------------
On 16 May 2001 21:19:36 -0400, Tom Hendricks
<112374.474@compuserve.com> wrote:

> I've suggested that a GC world may have preceded the RNA world that
>led to first life.
>
>    In looking at this website:
>http://www.kazusa.or.jp/codon/
>
[snip]

 I have given further thought to two points you have made. I think it
is quite possible the genetic code first came about in a high
temperature enviroment. While I would disagree with your idea of an
all GC world, I think that GC, as it applies to the early genetic code
evolution, could have been used much more in codons than AU.
 Since I will give my own views on some of this, note that I an not a
biologist just a computer programmer with an interest in evolutionary
theory.
 First some further background. In the 1980's it was noted that in
heat lovers (thermophilics) there was a strong preferential use of
thermally stable amino acids encoded by GC-rich codons(e.g. alanine
and arginine) and strong avoidance of thermally unstable amino acids
encoded by GC-poor codons (e.g. serine and lysine). Bernardi(1986)
looked at the same general data you have looked at and concluded the
very high CG seen was because for this reason. He saw the same
apparition you are seeing. The generally high CG content in
thermophilics is because of the mutational GC-pressure. One should be
able to see some effect of a preferential use of GC-rich amino acids
after subtracting the effect of mutational GC-pressure. I looked at 10
random thermophilics (6 high CG, 3 low CG, and 1 neutral)  and, while
difficult to remove the CG-pressure effect, it looks like they are
2-6% higher in CG content in the 1st and 2nd codon position that
otherwise expected. Someone has probably done analysis of all this
since 1986 but I am not aware of any information. Some other evidence
of an early preference for GC is the fact that rRNA is about 55% CG
and tRNA is about 60% CG. I should note that this mutational
AT-pressure or GC-pressure derives from errors in DNA copying. The
actual error rates are very very low, but the difference in the two
rates can greatly effect codon GC content, especiallly in semi-silent
3rd position.
  You also see a low GC in the 2nd codon position and higher GC on the
two end positions and give some arguments why this should be so. Again
I think you are off target. You are arguing that current state of GC
content in the 1st and 2nd codons indicate the state in the early
world just after the formation of the genetic code. I think you being
mislead here and the correlation is very low. In fact, I think all 3
codon positions would have been high CG or even very high GC in this
early world at the time of the formation of the genetic code. The
reason the 2nd codon now has low CG content and 1st codon only
slightly higher is because the CG content derives from the amino acids
they code for and the frequency of these amino acids in the population
of all proteins today. This frequency of use of amino acids was very
different in this early world. Today cells generally can build their
own amino acids but in this very early world they could not and would
therefore have a high preference for amino acids (or pre-built
components) that were naturally most available. So this frequency of
use of amino acids was different then than now.
  Let me now explain why I think the GC bond was so preferred in
codons in the early world when the genetic code was first seen.
  First let me clear, this early world was an RNA system not DNA.
Where before I talked of GC and AT-pressure and the difference between
very very low error copy rates, this is not the case anymore. In this
early world, error rates are now high both for the rna AU and GC. It
would seem quite plausible that because of the stronger, more stable
or more thermally stable GC bond that the copy error for AU would be
higher than that for GC. At this point in time there is no copy
correction system, the error rate is due only to the GC or AU bond
strength or stability or thermal stability, however you view this. 
  If the GC copies with less error there are some consequences. 1st of
all, simply because of the high copy error, there is a strong
preference for one position to be silent. If one position is silent it
cannot have copy error. If one position is silent then the other two
positions alone determine the amino acid. If only two positions are
read, then the total error copy rate is the sum of the error rate at
two positions. If all three positions are read, then the total error
for the codon is the sum of the error rates at all three postions. It
seems the third position went silent.
  In the universal genetic code half the time the 3rd codon position
is silent and the other half it is semi-silent. If the first and
second codon positions are both C and/or G, then the amino acid is
specified. In this case the third codon position is always silent.
  I'm going to use a simplified model where the third position is
treated as silent and only the first two positions are used.
Jukes(1981) proposed that the early genetic code may have had a
completely silent third postion with only 16 possible codings. I'm not
arguing his position and I don't think he used my argument for why
this system would prefer one to be silent, I just use this model
because it is simpler and I'm interested in the case of C and/or G the
first 2 positons.
 OK, in this model the most preferred of the 16 possible codons are
the all C and/or G, with the lowest copy error rate.
 CC-
 CG-
 GC-
 GG-
  The next 8 preferred would the those with 1 A or U and 1 G or C in
the first and second position.
  The last 4 would be preferred would be all A and/or U.

 There is also a preference hierarchy among the amino acids. I think
it is generally felt that Glycine and Alanine are the 2 most
preferred. These are found in the highest amounts, way above anything
else, in electrial dischange experiments under various conditions and
also found in the highest amounts in meteorites. These would be the
most preferred because they were the most available. Except for these
two amino acids it not so clear what the preferences would be.
 There have been arguments that a given amino acid may have in some
way had an affinity to its codon or anti-codon and therefore there was
some restriction or preference in coupling codons with amino acids. I
see nothing persuasive in these arguments. While maybe my argument
doesn't require total freedom in these couplings, I will take the
position that was freedom for any codon to couple with any amino acid.

 My argument is that I think you can mathematically show that if there
is a preference in the codon sequence and if there is a preference
among the possible amino acids and if you may couple any codon with
any amino acid, then the system is optimal when the most preferred
codon sequence is coupled with the most preferred amino acid and the
2nd preferred codon sequence with the 2nd preferred amino acid, etc.
 I have argued there are four clearly preferred codons all C and/or G,
taken in any order they are, CC-,CG-,GC-, and GG-. I have argued there
are two clearly preferred amino acids, Alanine and Glycine.
 So what do we actually have in the universal genetic code.
We have Alanine = GC-
        Glycine = GG-
 This as would be expected with the above logic. If you don't accept
that Alanine and Glycine were the among the four most preferred amino
acids, you can't draw the conclusion from the couplings that all C
and/or G was preferred . Even if you accept that Alanine and Glycine
were the among the four most preferred amino acids, there is still a
5% probabiliy that they could have coupled with all G and/or C codons
by chance. I am persuaded by the logic and the low 5% probability of
this occurring by chance.
 In passing note that
        Proline = CC- 
 Proline is found in both electrostatic experiments and meteorites.
       Arginine = CG-
 I would not have expected Arginine to be in the group of the four
most preferred amino acids but if there was a preference for a +
charged amino acid then the choice is Arginine or Lysine and, as
previously noted, Arginine is more thermally stable and Lysine is less
thermally stable. 
 Again, for all these four codons the third codon position is truly
silent. It does not matter what it is. 
  There are some other consequences if the system follows the above
logic. It is driven from two directions to make proteins
preferentially using these four amino acids and to a lesser extent the
next eight that are coded using GC at one of the first two positions
in the codon. First is the general preference for these amino acids.
Second, proteins made with these amino acids store the information for
making them in rna that is passed from generation to generation with
less error because of the greater use of GC bonds over AU. Of course,
this constraint does not exist today where the copy error rates are
very very low. Over time, as the copy error rate drops and as DNA is
used to store the information, the preference for GC over AU
disappears. Also the preference for amino acids changes as organisms
make the amino acids rather than utilizing naturally occuring
components or complete amino acids.
 I should note that even the silent 3rd codon position would go to
high CG because the mutational rate AU to GC would be higher than the
rate GC to AU.
 I wouldn't call this a GC world, but those early codons would have
had a lot of GC.