Cook's Molecular Biology
Basics 1
Question: do all lifeforms have consciousness?
The answer to this question, one needs to
account for much more than philosophy alone.
First one needs to be able to best define
what life itself is. Biologists consider
life (at least at this stage of history) to
possess the following attributes:
* Metabolism (the chemical reactions
that occur in an organism in order to maintain
further chemical reactions)
* Reproduction (the process in which
new individual organisms are produced)
* Enviromental adaptation (able to
structurally, behaviorally or physiologically
cope with stresses and pressures of the environment)
But some physicists on the other hand have
their own take on what defines life:
* Open or continuous systems able to reduce
their internal entropy through waste removal
But Cook had one major question in his pursuits
that encompassed all of the above required
classifications of life: what separates
any of the above from molecular machines?
Indeed, the difference between living entities
and machines is not made clear in the above
classifications. As artificial intelligence
is explored and better advanced in these times,
as well as ahead, one really sees it difficult
to find a true dividing line that separates
living organisms from "non-living"
machines. How is a coal-based electrical power
plant any different than a living organism
in this sense with we humans being analagolous
to cellular mitochondria keeping everything
in motion from the inside? The real question
that Mr. Cook asked himself before his studies
in Synthetic Life began was when is a true-point
defined in the process of the creation of
life where consciousness is created?
Understand that and the rest of
the divisions fall comfortably into place,
or so he contends.
However, before this study is presented,
one really needs to follow the path from Physics
to Inorganic Chemistry to Organic
Chemistry then into Diminutive Biology.
It is indeed the link between Organic Chemistry
and Diminutive Biology where non-living chemicals
cross the threshold into full-fledged living
organisms. So where one probably should begin
is with a brief physical introduction, and
then he or she can better move along the line
as Mr. Cook did up to the point where Sythetic
Lifeforms were actually developed.
If the study of Synthetic Life were considered
a cancer, then the mole would best
be where we should begin. No...not that
kind of mole, silly; rather, the SI base unit
that measures the amount of substance.
Since atoms and molecules are cleary quite
small in comparison to the weights used in
common experiments, scientists simply consider
a large quantity of atoms or molecules in
their formulations. How many atoms, molecules
or elementary particles exactly are in a mole?
Why there are approximately 6.02214 X 10^23
of them, where 6.02214 X 10^23 is of course
known as Avogadro's Number.
Don't we all wish we had such an important
number like that named after us?
If you have first read over Cook's
Physics 101 class, you will have learned
all about dimensions. A mole is a dimension
in its own right. However, the unit more often
referred to in actual experimentation is how
many moles are in a defined amount of volume.
Quite simply, one asks, "how many moles
of such and such do I have in this container?"
Such a dimension is considered more of a state
of being called, "molarity."
Thus, molarity is of course in mol
/ L, where L is the unit of
liters (or litres if you're reading from across
the Atlantic). The letter M represents
the relationship of M = mol
/ L. This is so incredibly simple that
it still angers me violently today to remember
how complicated my high school chemistry teacher
explained it to us back then. But it's really
no more complicated than saying, if I have
10 eggs left in the egg carton, then the molarityish
state of the carton = 10 eggs / carton.
Simple!
Now, let us hereby discuss the structure
of the atom and pass this mole stuff behind
for the time being.
Scientists typically consider the nucleus
of an atom to range between 10^-15 meters
and 9.4 X 10^-15 meters. They also typically
consider the nucleus to contain the proton,
even though Mr. Cook considers the proton
to orbit such a region about 2 1/6 X 10^4
times that...at least in the Hydrogen atom.
But this will not be a factor really in this
study. We care not about the nucleus of the
atom in chemistry, as it is the outermost
electrons that take part in chemical
reactions. These important electrons exist
in what is called the Valence Shell
of the atoms. Thus, the electrons located
in this region are referred to as Valence
Electrons. Go figure. And the electrons
in this shell determine exactly how one element
reacts with another, occuring simply by removing
or adding electrons from this region. Yeah,
atoms don't much like to have their electrons
removed, so they react aggressively to get
them back, sometimes violently if provoked
enough. And when an atom does have
some or all of its electrons removed from
the valence shell, chemists call this an "open
shell." Can't really consider it
an empty shell, as it very well may
not be completely empty in all cases. So its
just called "open." Gee, those chemists
sure are clever in their terminology, huh?
And in the case of an atom existing with an
open shell, the atom or molecule is no longer
passed off as an atom or molecule at all anymore,
which is probably why atoms hate so much for
their electrons to be removed. Ahem... Such
atoms or molecules are considered at this
point to be cations. While this of
course is not a disparaging term the least
bit, small particles tend to get offended
at the thought of being naked ions and fight
with all their might to get electrons back
in a hurry; that is, if other electrons are
readily available. If not, then they tend
to sit and wait patiently in the solution
for any possible change that may free some
up.
Now, sometimes atoms and molecules get greedy
and grab more electrons than they deserve.
Needless to say, cations find this quite disturbing
and react extra violently with these types.
The atoms carrying more electrons than they
need are called "anions."
And while both cations and anions are both
referred to as ions, and can react
with each other in just about any condition,
it takes temperature/energy variations
to get either of them to react with regular
ole' balanced atoms and molecules. This reaction
can lead to various outcomes, but often into
what is called a covalent bond. It
may seem like a complicated concept from the
term but it really isn't at all. It's the
just a state of being where atoms and molecules
share two electrons from their valence shell.
It perhaps is more of a tug-o-war scenario
than a bond, considering the degree of their
forces and the fact that they can react as
well under any subtle change. It's as if the
two atoms have exactly equal strength and
are simply waiting for the other to make a
move for it to loosen its grip on the electron/s.
Since such covalently bonded atoms or molecules
can react at the drop of the hat, they too
are considered ions, more specifically, polyatomic
ions, meaning of course...more than one
atom.
Ever see a basketball game where several
members from opposing teams all get a grip
on the ball and won't let go until the ref
interferes. It's actually a very similar process.
In fact, such a polyatomic bond can contain
several molecules or atoms all fighting over
the same electrons. Generally though, polyatomic
ions function as a single unit and are stable
in their tug-o-war formation so long as no
other electrons are available. Covalent bonds
are not necessarily ionized, as the overall
charge may be balanced so long as they
are both holding onto the same electrons.
Now, a most interesting fact of these so-called
bonds that most people, including top chemists,
do not always consider is the fact that when
these atoms or molecules are pulling on an
electron, they actually weigh less!
This is all due to Einstein's wonderful E=mc^2.
Don't believe it? Well, don't take anyone's
word for it; demonstrate this effect yourself.
Place a typical scale in front of a solid
bar, railing or other means of grip. Stand
on the scale. Then, keeping your feet solidly
placed on the scale, pull toward the railing
at a 90 degree angle from the ground in the
same way a proton pulls on an electron at
90 degrees. You will easily notice, depending
on how hard you pull, you just lost
10 to 15 pounds or more. Now try the same
thing by pushing on the railing and you will
notice that you gained exactly 10 to
15 pounds or more in equal but opposite relation.
Some of your mass was converted to energy
in the relationship of Equation
(16) as shown in the NET pages. So, in
accordance with Mr. Cook's NET, this dimension
is called Inertiance, the state of
weight gain or loss dependent upon its steady
push or pull, which of course has to do with
it's charge. And inertiance is in C^2 (coulombs
squared). When an electron is bonded to an
atom, its centrifugal force from its orbit
tends to pull it outward from the nucleus
at 90 degrees in the simplest case. The proton
is pulling at the electron from the center
so the overall weight is less than if their
masses were simply added. See, 1+1 does not
always equal 2. In terms of mass, 1+1 <
2.
Aye, screwy stuff, but very important and
required for all of nature to exist as we
see it today.
Now, let's slowly begin to step away from
physics terminology and down to possibly the
most important ion in all of the study of
chemistry. Actually, it's really not an ion
at all. In hydrogen there is only one electron
and one proton, right? Take away the electron
and you really don't even have an atom
any more; thus, we cannot very well consider
it an ion. It's just a proton! That being
said, chemists still like to consider it an
ion, as this is the only exception from the
periodic table. Thus, they call a proton H+,
AKA a Hydron or more often a Hydrogen
Anion. Argh! This is why chemists and
physicists really should get together more
often. So, while the rest of the world knows
it's just a proton, chemists need to class
it as an anion, else they risk falling into
a state of mad confusion keeping everything
in order with all the nomenclature they use.
In any case, when one H+ (hydron/proton) joins
up with an atom, molecule or other ion, the
process is called "protonation."
Thus, the atom, molecule or ion is said to
be protonated. Pretty simple, right? Well,
it should be simple, as this is perhaps the
most fundamental of all chemical reactions.
It is the basis of everything to follow. First
comes mathematics, then physics, and then
protonation leads our studies right into the
peculiar full-blown world of chemistry.
Shall we take that journey together...
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