>>>David Bowman: No matter what apparatus is or is not needed to enable a
given process, the 2nd law is obeyed as usual, and isn't violated nor
"overcome".
DNAunion: I will respond to other stuff later. This caught my eye yesterday
but I just found time to whip something up today when I got home from work.
I started writing to explain - once again - my use of the work overcome, but
kept going after that. This was all written in very short span of time: I
don't claim it is perfect. But it may still be helpful.
Teeter-totter Analogy ("Overcome")
Another useful analogy for the use of the term "overcome" in this chapter
involves the common playground see-saw (or teeter-totter). Let us assume
that the two "arms" (the two extensions - one to the left and one to the
right - that have at their distal portions the seats on which people usually
sit, but which in this model, have identical hand-woven baskets mounted on
them to store objects) of the teeter-totter are equal in length and weight
and that the overall apparatus is perfectly balanced. Furthermore, let us
assume that no forces are acting on the system (teeter-totter) except for
those mentioned (i.e., there are no hurricanes, volcanoes, steam engines,
motors, pulleys, etc. that could affect the see-saw). In the starting setup,
the seats of the sea-saw are empty so the two arms are perfectly level.
From the neutral starting position, suppose one were to place a 10-lb. bag of
sugar in the basket on the right-hand seat. The balance would shift and the
teeter-totter's right arm would dip such that it made contact with the
ground, following the tendency gravity imposes on small mobile aggregates of
matter to be moved physically toward much more massive and stationary
aggregates of matter (i.e., everyday gravitational attraction). The downward
movement of the bag/basket/seat would represent a "downhill" process: one
that can occur spontaneously: one that would be in the allowed direction.
Once at the bottom, the bag would remain there. Movement in the opposite
direction - the bag/basket/seat rising - would represent an "uphill" process:
one that could not occur spontaneously; one whose direction would not be
allowed. There would be no way for the bag to become elevated by itself: for
it to rise, something else would have to exert an influence on the
teeter-totter system.
Let us consider next what would happen were one to begin placing snowballs
into the basket on the left-hand seat. There would then be a second
tendency: for the side with the sugar to *rise* from the ground. But if only
one pound of snowballs were placed in the left basket, the bag of sugar would
remain firmly planted on the ground: the tendency of the one pound in the
left basket to raise the 10-lb bag of sugar in the right basket would not be
enough to *overcome* - that's right, *overcome* - the tendency the seat with
the 10-lb bag of sugar would have for being as close to the Earth's surface
as physically possible. But were that person to continue adding more and
more snowballs, then the weight on the left arm would begin to approach 10
pounds. The right seat would have more of an overall, combined tendency to
become elevated, and motion in the formerly disallowed direction would begin.
With a full 10 pounds of snowballs in the left basket, the right seat would
become elevated to its original position, level with the other seat. The
tendency that gravity would have been forcing upon the bag of sugar
throughout - to remain as close as physically possible to the Earth's surface
- would have been overcome: if it hadn't, the seat with the bag on it would
have continued to "eat dirt".
Note that *nowhere in this intuitionally-infallible analogy is gravity
violated, defied, cancelled, broken, or done away with, not even for a
nanosecond*. This is the sense in which the word "overcome" is being used in
this chapter. There is a primary tendency in one direction - the downhill,
spontaneous direction - imposed on matter by a basic law of nature, which
becomes influenced by another tendency in the opposite direction. If the
second tendency becomes sufficient ("strong enough") to cause the process to
proceed in the originally-disallowed direction, then that second tendency has
overcome the original one. The original tendency still exists - and existed
throughout - and is still influencing the system - and influenced the system
throughout - just not as strongly as the new force/tendency.
Teeter-totter Analogy (Amino Acid Synthesis vs. Protein Synthesis)
Let us extend this analogy further. Starting again with a balanced, level
teeter-totter, let someone place a bag of sugar on the right seat. Again,
the right seat falls towards the Earth until it makes contact. But this
time, we are assigning this downhill process, that occurs spontaneously, in
the allowed direction, to the synthesis of amino acids. Amino acid formation
from simpler molecules is an exergonic reaction under many sets of
naturally-occurring conditions). Once at the bottom, the sugar would remain
there. Likewise, amino acids would remain amino acids - well, that is, their
becoming polymerized into polypeptides would not occur as doing so would
represent a decrease in entropy: dehydration synthesis is an uphill process:
analogous to the unaided rising of the bag of sugar: both are in the wrong
direction and neither will occur spontaneously. Next, we call upon outside
assistance again, allowing the placing of snowballs on the other seat. This
external "force" represents some *unspecified organizing force/mechanism*
that assembles the amino acids into polypeptides. With this assistance, the
sugar could rise, and, by analogy, the amino acids could become joined
together into long chains. At this point in the analogy, the tendency for
the bag of sugar to remain as close to the ground as possible - and for the
amino acids to remain individual, unlinked units - has been overcome.
The question remains, what was the *unspecified organizing force/mechanism*
relied upon in the analogy? In extant cells, it is ribosomes and all their
related biochemical entities: they take individual, unlinked amino acids and
bond them together to form polypeptides. The catalytic core of the ribosome
(peptidyl transferase) is composed solely of rRNA. So RNA is the first
component of the *unspecified organizing force/mechanism* that is used to
overcome the natural tendency amino acids have for remaining unlinked. RNA
itself is composed of (1) nucleobases (the four nitrogenous bases: two
purines and two pyrimidines), (2) units of the pentose (5-carbon sugar)
ribose, and (3) phosphate groups. For this brief discussion, the other
components required for protein synthesis in extant cells (proteins that
charge tRNA molecules, other proteins that assist in elongation, DNA from
which the mRNA is transcribed, and the proteins that function during that
transcription, etc.) will not be considered; the current list (adenine,
guanine, cytosine, uracil; polyphosphates; D-ribose; *all of which must occur
in precise physical and sequential arrangements*) is enough to demonstrate
that protein synthesis is not a simple thermodynamic process, such as the
cooling of a hot cup of tea.
So the mechanisms and coupled processes that allow amino acids to overcome
their natural tendency for remaining individual, unlinked entities, and to
instead forge up the polymerization hill, are well known and understood.
That is, at least for extant cells. The question remains, what exactly were
the currently *unspecified organizing forces/mechanisms* on the prebiotic
Earth that allowed for biologically-relevant protein synthesis?
Teeter-totter Analogy (Steady State)
When we left our see-saw analogy, the bag of sugar had been elevated back to
its original position with the assistance of an external force/tendency,
imposed on the system by the counter-balancing weight of many snowballs. But
the natural tendency for the sugar to move towards the Earth still existed,
and still exerted an influence on the system. This time, the side with the
bag of sugar represents the metabolism of a cell. The natural tendency is
for chemical and biochemical reactions to reach thermodynamic equilibrium: if
left to themselves, they would all move only in the allowed, downhill
direction.
So let us contemplate what would happen to this teeter-totter system were it
in a hot, dry environment. Obviously, the snowballs would melt fairly
rapidly, with the water running out of the hand-woven baskets and off the
seat, becoming useless in the struggle to maintain the sugar in its elevated
position. This reduction in the weight of the snowballs is analogous to the
naturally-occurring reduction in free (i.e., useable) energy in a system; for
example, by the dissipation of energy as heat.
As the snowballs continued to melt, the weight of that side would steadily
decrease, reducing the influence the left side exerted on the right side, and
the result would be that the seat with the bag of sugar would end up back on
ground. For a bag of sugar, this fate is not that dramatic. But the
analogous situation for cell - where its biochemical reactions have reached
equilibrium and there is no more free energy to perform work on the system -
is devastating: life would cease.
In order to maintain the bag of sugar in its elevated position, one would
need to continuously and actively intervene by placing additional snowballs
on the left hand side to compensate for their continuous melting. There
would be an ongoing, continual, and active *struggle* to maintain the sugar
elevated above its natural state. The same applies to the biochemical
reactions that sustain life. Left to themselves, they would follow their
natural tendency towards reaching thermodynamic equilibrium. To avoid this
deadly fate, cells must continually and actively invest resources into
replacing proteins and regenerating ATP (among other things, such as
expelling wastes and taking in energy and nutrients), neither of which is
itself a spontaneous reaction: both are uphill, endergonic processes. In
cells, there is an ongoing, continuous, active struggle to overcome the
natural tendency for biochemical reactions to reach equilibrium; and to
struggle to continually decrease the entropy (increase the order) inside the
cell by manufacturing proteins and nucleic acids (again, both uphill
processes) to replace the damaged proteins and nucleic acids that suffer at
the hands of natural processes.
Teeter-totter Analogy (ATP)
So far, the teeter-totter system is in no real danger: we just need someone
to continually plop new snowballs into the left-hand basket. But to keep
this as natural as possible, we need to eliminate the person who magically
forms snowballs and elevates them so that they can be placed inside the
basket (after all, there are no real Maxwell's demons of sorts running around
inside cells whipping up energy from thin air, or exerting forces that were
created ex nihilo). Instead, the snowballs themselves have to be raised on
other nearby see-saws to a height where they can be transferred laterally
into the basket of interest (we will neglect the "work" associated with
moving the snowballs in a purely horizontal direction). Thus, our
teeter-totter (let us call it TT1) is associated with many others in a
playground. Each snowball that is to be added to the basket on the left arm
of TT1, must first be elevated from the ground on its own teeter-totter (TT2,
TT3, etc.) before it can be of any use.
One might be curious concerning what the snowballs represent in this analogy.
ATP - the energy currency of cells. ATP is used in cells to drive
thermodynamically-unfavorable reactions; it couples energy-liberating
processes (in our analogy, the lowering of a seat) with energy-consuming
reactions (in our analogy, the raising of a seat), but has itself to be
synthesized, which is an uphill process (analogous to the arm of TT2 rising
from the ground with the snowball in its basket). So ATP synthesis will not
proceed either unless it is coupled to something else (the flow of protons
through an ATPase). That is sort of like saying snowballs will not be raised
on their teeter-totters unless ice cream is placed on the counter balancing
arm of their own teeter-totters. But the ice cream itself must be elevated
on its own teeter-totter in order to elevate the snowball so that it can be
placed in the elevated basket of the sugar teeter-totter: how does the ice
cream get elevated? Is this in any way analogous to what occurs in cells?
Yes. Protons will not flow through the ATPase to power ATP synthesis unless
a proton gradient exists between the inside and outside of the mitochondrial
membranes (sticking to eukaryotes). What generates the proton gradient?
Electrons "falling down" an electron transport chain. So to cut the analogy
short, the bag of sugar cannot be raised unless snowballs are placed in the
opposing basket, but snowballs cannot be placed in the opposing basket unless
they are raised, which cannot occur unless ice cream is placed in the basket
opposite the snowballs on TT2, and the ice cream cannot be placed in the
basket opposite the snowballs on TT2 unless they are raised, which will not
occur unless frozen yogurt is placed into the basket opposite the ice cream
on TT3. So in this system, a continual supply of frozen yogurt must be
furnished or the whole complex of see-saws grinds to a halt. This level of
interdependence is far below that found in the simplest cells. For life to
exist, numerous and varied "see-saws" must form intricate, interconnected and
interdependent webs, where every uphill reaction is coupled to one or more
downhill reactions, which themselves require uphill processes to push them up
to a high-enough level, and the whole "playground-full of see-saws" must be
kept "off the ground" at all times. Again, the thermodynamics struggles
associated with life are far more complicated and involved than that of a hot
cup of tea cooling.
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