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# Last Update: 6 December 2017

Biology Part II
& M 118

## The Concept of Thermodynamics

Thermodynamics (from the Greek thermos meaning heat and dynamis meaning power) is a branch of
physics that studies the effects of changes in temperature, pressure, and volume on physical systems at the
macroscopic scale by analyzing the collective motion of their particles using statistics. Roughly, heat means
"energy in transit" and dynamics relates to "movement"; thus, in essence thermodynamics studies the
movement of energy and how energy instills movement. Historically, thermodynamics developed out of the
need to increase the efficiency of early steam engines.

An important concept in thermodynamics is the system. A system is the region of the universe under
study. A system is separated from the remainder of the universe by a boundary which may be imaginary or
not, but which by convention delimits a finite volume. The possible exchanges of work, heat, or matter
between the system and the surroundings take place across this boundary. There are five dominant classes of
systems:

1. Isolated Systems matter and energy may not cross the boundary.
2. Adiabatic Systems heat may not cross the boundary.
3. Diathermic Systems - heat may cross boundary.
4. Closed Systems matter may not cross the boundary.
5. Open Systems heat, work, and matter may cross the boundary.

For isolated systems, as time goes by, internal differences in the system tend to even out; pressures and
temperatures tend to equalize, as do density differences. A system in which all equalizing processes have
gone practically to completion, is considered to be in a state of thermodynamic equilibrium.

## In thermodynamic equilibrium, a system's properties are, by definition, unchanging in time. Systems in

equilibrium are much simpler and easier to understand than systems which are not in equilibrium. Often,
when analyzing a thermodynamic process, it can be assumed that each intermediate state in the process is at
equilibrium. This will also considerably simplify the situation. Thermodynamic processes which develop so
slowly as to allow each intermediate step to be an equilibrium state are said to be reversible processes.

## The laws of thermodynamics

In thermodynamics, there are four laws of very general validity, and as such they do not depend on the
details of the interactions or the systems being studied. Hence, they can be applied to systems about which
one knows nothing other than the balance of energy and matter transfer. Examples of this include Einstein's
prediction of spontaneous emission around the turn of the 20th century and current research into the
thermodynamics of black holes.

## Zeroth law of thermodynamics, stating that thermodynamic equilibrium is an equivalence relation.

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If two thermodynamic systems are in thermal equilibrium with a third, they are also in thermal
equilibrium with each other.

## First law of thermodynamics, about the conservation of energy

The increase in the energy of a closed system is equal to the amount of energy added to the system
by heating, minus the amount lost in the form of work done by the system on its surroundings.

## Second law of thermodynamics, about entropy

The total entropy of any isolated thermodynamic system tends to increase over time, approaching a
maximum value.

## Third law of thermodynamics, about absolute zero temperature

As a system asymptotically approaches absolute zero of temperature all processes virtually cease and
the entropy of the system asymptotically approaches a minimum value.
See BoseEinstein condensate and negative temperature.

Thermodynamic potentials
As can be derived from the energy balance equation on a thermodynamic system there exist energetic
quantities called thermodynamic potentials, being the quantitative measure of the stored energy in the
system. The four most well known potentials are:

Internal energy

Enthalpy

## Gibbs free energy

Potentials are used to measure energy changes in systems as they evolve from an initial state to a final state.
The potential used depends on the constraints of the system, such as constant temperature or pressure.
Internal energy is the internal energy of the system, enthalpy is the internal energy of the system plus the
energy related to pressure-volume work, and Helmholtz and Gibbs free energy are the energies available in a
system to do useful work when the temperature and volume or the pressure and temperature are fixed,
respectively.

## Quotes & humor

A common scientific joke, as stated by C.P. Snow, expresses the four laws simply and surprisingly
accurately as:

## Zeroth: "You must play the game."

First: "You can't win."
Second: "You can't break even."
Third: "You can't quit the game."

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Laws of Thermodynamics
Energy exists in many forms, such as heat, light, chemical energy, and electrical energy. Energy
is the ability to bring about change or to do work. Thermodynamics is the study of energy.

First Law of Thermodynamics: Energy can be changed from one form to another, but it cannot
be created or destroyed. The total amount of energy and matter in the Universe remains
constant, merely changing from one form to another. The First Law of Thermodynamics
(Conservation) states that energy is always conserved, it cannot be created or destroyed. In
essence, energy can be converted from one form into another. Click here for another page
(developed by Dr. John Pratte, Clayton State Univ., GA) covering thermodynamics.

The Second Law of Thermodynamics states that "in all energy exchanges, if no energy enters
or leaves the system, the potential energy of the state will always be less than that of the initial
state." This is also commonly referred to as entropy. A watchspring-driven watch will run until
the potential energy in the spring is converted, and not again until energy is reapplied to the
spring to rewind it. A car that has run out of gas will not run again until you walk 10 miles to a
gas station and refuel the car. Once the potential energy locked in carbohydrates is converted
into kinetic energy (energy in use or motion), the organism will get no more until energy is input
again. In the process of energy transfer, some energy will dissipate as heat. Entropy is a measure
of disorder: cells are NOT disordered and so have low entropy. The flow of energy maintains
order and life. Entropy wins when organisms cease to take in energy and die.

## Second Law of Thermodynamics

The second law of thermodynamics is a general principle which places constraints upon the direction of
heat transfer and the attainable efficiencies of heat engines. In so doing, it goes beyond the limitations
imposed by the first law of thermodynamics. It's implications may be visualized in terms of the waterfall
analogy.

## The maximum efficiency which can be achieved is the Carnot efficiency.

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Second Law: Heat Engines
Second Law of Thermodynamics: It is impossible to extract an amount of heat QH from a hot reservoir and
use it all to do work W . Some amount of heat Q C must be exhausted to a cold reservoir. This precludes a
perfect heat engine.

This is sometimes called the "first form" of the second law, and is referred to as the Kelvin-Planck statement
of the second law.

## Second Law: Refrigerator

Second Law of Thermodynamics: It is not possible for heat to flow from a colder body to a warmer body
without any work having been done to accomplish this flow. Energy will not flow spontaneously from a low
temperature object to a higher temperature object. This precludes a perfect refrigerator. The statements about
refrigerators apply to air conditioners and heat pumps, which embody the same principles.

## Second Law: Entropy

Second Law of Thermodynamics: In any cyclic process the entropy will either increase or remain the same.

## a state variable whose change is defined for a reversible process at T where

Entropy:
Q is the heat absorbed.
Entropy: a measure of the amount of energy which is unavailable to do work.
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Entropy: a measure of the disorder of a system.
Entropy: a measure of the multiplicity of a system.

Since entropy gives information about the evolution of an isolated system with time, it is said to give us the
direction of "time's arrow" . If snapshots of a system at two different times shows one state which is more
disordered, then it could be implied that this state came later in time. For an isolated system, the natural
course of events takes the system to a more disordered (higher entropy) state.

## Energy and Order in Biological Systems

The concept of entropy and the second law of thermodynamics suggests that systems naturally progress
from order to disorder. If so, how do biological systems develop and maintain such a high degree of order?
Is this a violation of the second law of thermodynamics?

Order can be produced with an expenditure of energy, and the order associated with life on the earth is
produced with the aid of energy from the
sun.

## For example, plants use energy from the

sun in tiny energy factories called
chloroplasts. Using chlorophyll in the
process called photosynthesis, they convert
the sun's energy into storable form in
ordered sugar molecules. In this way,
carbon and water in a more disordered state
are combined to form the more ordered
sugar molecules.

## In animal systems there are also small

structures within the cells called
mitochondria which use the energy stored in sugar molecules from food to form more highly ordered
structures.

## The second law of thermodynamics and evolution

Many fundamentalist Christians see the theory of evolution as a threat to their faith, evidently
because it is not explicitly included in Genesis. (They also misunderstand the scientific application
of the word "theory" that the chemist uses in discussing atomic theory or the kinetic molecular
theory of gases, ideas as unquestioned by all chemists as evolution is by professional biologists.)
This is tragic because it cuts off sincere individuals who are not scientists from understanding the
powerful relevance of one of the most important concepts in all of science.

Most disquieting to chemists who are interested in thermodynamics are the misleading statements
about the second law and chemistry that creationist spokespeople have made. A few emphases
from previous pages in the present Web site and from www.secondlaw.com that bear on this

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presentations of the second law of thermodynamics and its irrelevance to creationists arguments
against evolution.

"A watch must have required a watchmaker; a car could not have formed itself from parts."

(The following includes some excerpts from the previous section, "Obstructions..")

The above statements in italics from creationists are certainly true, but they have nothing to do
with the behavior of atoms and molecules. Car parts in a junkyard dont speed inside the yard at a
thousand miles an hour, constantly colliding with each other, fusing together with a similar part (or
different ones) so violently that enormous quantities of energy are given out enough to make
them white hot.

Why give a silly illustration like that? Anyone knows that it is not an inherent quality of metal parts
to spontaneously join with similar or quite different parts to form complex new arrangements. Yet,
this IS precisely the normal behavior of most of the chemical elements that constitute the world
and the universe. The value of the second law of thermodynamics is that it quantitatively describes
the energetic aspects of the chemical elements and the compounds they form. The chemical
potential energy (the enthalpy of formation) that is bound in most of the 20,000,000 known kinds of
molecules is less than that in their elements. Thus, energetically , the second law says that the
majority of compounds now known could spontaneously form from the corresponding elements. In
complete contrast, watches or cars are not lower in thermodynamic energy than the total energy of
their individual components. Therefore, the second law says that it is totally inappropriate to
compare them with the behavior of chemical compounds and elements.

Incessantly moving at a few hundred to two thousand miles an hour at ordinary temperatures.
hydrogen and many other atoms behave in a fashion that is impossible for car parts: Most atoms
spontaneously "bond" when they vigorously collide, forming extremely powerful associations in
very specific ways. These new arrangements can be molecules so stable that temperatures of
thousands of degrees can't tear them apart again. Molecules are not atoms randomly stuffed in a
package. When three or more atoms join to form a molecule, they are arranged in precise order,
normally unchanging over time, and with a relatively fixed geometric relationship.

Finally, many kinds of molecules can strike other kinds very violently and produce totally new
types of molecules another mode of formation of new complex ordered structures due to the
same innate nature of atoms to form strong bonds and spread out energy to the surroundings.
Amino acids when simply melted with other amino acids (to make them move more rapidly) form
huge new compounds. These are NOT useful or valuable proteins. The process simply illustrates
the probability of the existence of complex gigantic substances in nature. Though not proteins,
they are "proteinoid" in that they have hundreds to thousands of amino acid units firmly joined in
the same kind of bonds that hold proteins together.

A simple example of the spontaneous behavior of elements is the reaction of hydrogen gas with
oxygen (that was tragically illustrated when the Hindenburg dirigible burned in 1937). Hydrogen
atoms have such a great inherent tendency to form strong bonds with oxygen to yield water that a
small energy of activation, in the form of a spark affecting only a relatively few molecules, causes
the two substances to start to react, resulting in an enormous evolution of energy. This is exactly
as the second law predicts: some of the energy in a mixture of hydrogen and oxygen becomes
spread out (so much and so rapidly that it is an explosion) when the lesser energetic compound,
water, is formed. Yet, water is more complex than the simple elements and its atoms are arranged
in an exact geometric pattern.

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There are millions of compounds that have less energy in them than the elements of which they
are composed. That sentence is a quiet bombshell. It means that the second law energetically
FAVORS yes, predicts firmly the spontaneous formation of complex, geometrically ordered
molecules from utterly simple atoms of elements. Popular statements such as "the second law
says that all systems fundamentally tend toward disorder and randomness" are wrong when they
refer to chemistry, and chemistry precisely deals with the structure and behavior of all types of
matter.

To summarize this important conclusion that is known by very few who are not chemists:
Energetically, the second law of thermodynamics favors the formation of the majority
of all known complex and ordered chemical compounds directly from their simpler
elements. Thus, contrary to popular opinion, the second law does not dictate the
decrease of ordered structure by its predictions. It only demands a "spreading out"
of energy when such ordered compounds are formed spontaneously.

Also, to repeat a caution: The foregoing only describes energetic relationships involving the
second law. It does not mean that most complex substances can be readily synthesized
just by mixing elements and treating them in some way. The second law has nothing to do
with pathways or procedures of synthesis.

Most complex molecules may require the expertise of one or of many chemists to put them
together in a laboratory. However, so far as the second law of thermodynamics is concerned, not
only water but cholesterol, DNA, the anti-depressant in St. Johns Wort and millions of other
complex substances contain less energy than their constituent elements. Therefore,
thermodynamically, their formation from those elements would be a spontaneous process,
energetically favored by the second law.

## "The Law of Disorder"

As part of their attempts to challenge evolution, some religious writers have included comments to
the effect that the second law what they have called "the law of disorder" strictly prohibits the
chance formation of complicated stuctures from simple parts, including complex molecules from
simple ones. This site, and especially http://www.secondlaw.com, have shown repeatedly that it is
fallacious to view the second law as a predictor of disorder. The second law concerns energy, not
patterns of objects. The second law states that energy tends not to be restricted to one or a few
energy levels in atoms and molecules, but to be dispersed to as many such levels as possible
rephrased in homely terms involving molecules, "Intense or concentrated energy tends to spread
out and diffuse".

In that spreading-out process, macro objects sometimes are displaced and moved to random
arrangements that humans subjectively define as "disorder". A violent wind not only can break a
window in a building and blow the papers in an office all over a square mile, but also destroy the
building itself. However, this is an incidental consequence of dispersing and spreading out of the
energy in a tornado, not an event that is due to the innate nature or behavior of inanimate objects
themselves in the absence of such an energy flow. Moving common objects around so they fall in
disorder is a singular and accidental aspect of the universal tendency of energy to diffuse, not the
general thrust or meaning or requirement of the second law that applies to objects.

Further, as described in the first section of this website, the second law is a tendency, not an
instantly effected edict. Its predictions might not come true for millions or billions of years. These
kinds of delay are due to the second law being obstructed and hindered by what chemists call
"activation energies". All the biochemicals in our bodies except inorganic substances are protected
and kept from oxidation or other disastrous reaction by activation energies. Almost all the
materials from which our orderly prized artifacts are made are similarly kept from rapid oxidation in

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air. The second law is a powerful generality, but it is often blocked (to our human advantage) in
chemical substances, chemical reactions, and physical events in everyday life.

"The second law says that complicated molecules cant form spontaneously"

(This question is treated in greater detail and more technically in the last half of the previous
section, "Obstructions to the second laws make life possible")

Of course, the most complex substances that we know are produced by organisms. The
photosynthetic example often cited by creationists is as follows: Trees make sugars and cellulose
as well as the green chlorophyll and other colored chemicals that we see in Fall leaves, among
hundreds of other compounds. They use energy from sunlight by means of intricate chemical
processes to synthesize the complex higher-energy content substances just mentioned from
lesser energy compounds like carbon dioxide and water. But the second law says that the
opposite process of higher-energy compounds changing into lesser-energy substances is what
tends to happen by itself, spontaneously, without outside aid from any energy source. Therefore,
photosynthesis is a thermodynamically non-spontaneous process.

Religious writers are familiar with the general process of photosynthesis but are unskilled in
dealing with chemical thermodynamics. They claim that the second law not only says that it is
impossible for more complex substances to be spontaneously formed from simpler materials, but
also a non-spontaneous process like photosynthesis that produces complex substances requires
the presence of an organism, such as a plant.

Neither claim is true. As has been discussed adequately in a previous portion of this essay about
the second law and evolution, "A watch must have a watchmaker", the spontaneous formation
of millions of far more complex compounds than their elements is energetically favored by the
second law. This is true whether the new molecule is more or less complicated than its starting
materials because the second law is concerned only with energy. All other requirements or
consequences are not within the purview of the law.

## It is equally erroneous to state that complex substances cannot be formed non-spontaneously

from simpler without the intervention of an organism, "a patterning mechanism". Again, as has
been discussed, the formation of patterned molecules is inherent in the nature of atoms combining
with one another, no external template or help from a living organism is required by any physical
law. "Non-spontaneous" simply means the addition of energy to a system of elements or
compounds during the process of forming a new compound. Chlorophyll and substances as
complex as chlorophyll have been synthesized in the laboratory, in glass vessels without the
presence of any organisms in the reaction. Although that process was extremely difficult and took
many person-years to complete, the principle was clear long before the chlorophyll project was
undertaken: The non-spontaneous syntheses of greater-energy, complex substances from lesser-
energy simple molecules without the aid of organisms is not prevented by the second law. It is just
not favored. Over the past two centuries, millions of complex substances admittedly less so
than chlorophyll have been made similarly in laboratory glassware without the need for
organisms.

## The spontaneous and non-spontaneous formation of complex compounds in space

Finally, it should be recognized that both spontaneous and non-spontaneous reactions to form
complex substances are common in outer space. The two most prevalent elements there are
hydrogen and carbon with considerably smaller quantities of oxygen and nitrogen. Although
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relatively few atoms or molecules are present per cubic inch, in untold quadrillions of cubic miles
of space there are many millions of tons of each.

Organic compounds are those substances that contain carbon. (Because they differ so much from
organic compounds in their properties, carbon monoxide, dioxide and the carbonates are not
included.) The simplest organic compounds, called alkanes and composed only of carbon and
hydrogen, contain portions or sections with one carbon atom holding two or three hydrogen atoms.
Spectroscopic evidence for these characteristic alkane sections has been found throughout space.
All alkanes are all lesser in energy than their elements. (Structures are in:
http://www.nyu.edu/pages/mathmol/library/hydrocarbons/ ). Therefore, the second law says
irrefutably that they could be formed spontaneously from carbon and hydrogen with the net
evolution of energy. Their structural pattern is not vastly complex but it is far more so than that of
individual elements.

Far more complicated types of compounds that contain either carbon and hydrogen alone, or
those elements with oxygen, have been detected in space: PAHs, polycyclic aromatic
hydrocarbons. The thermodynamic category of formation of the two groups of PAHs are different.
IF oxygen is present in the PAH ( and this cannot yet be decided spectroscopically ) the
substances are less energetic than the carbon, hydrogen, and oxygen elements from which they
were formed. Thus, they were formed spontaneously strictly in accord with the second law of
thermodynamics.

It is an amusing sidenote that the anti-depressant ingredient in St. Johns Wort, listed as hypercin
and the precise structure given in the Merck Index, is an oxygen-containing PAH. These are
complex substances that are important here on earth. It is still questionable, of course, that
molecules with this precise structure are in space, but it is energetically completely possible that it
and many comparable materials may be present there.

PAHs composed only of carbon and hydrogen contain more energy within their molecules than do
elemental carbon and hydrogen. Therefore, their synthesis from the elements is
thermodynamically non-spontaneous. Nevertheless, these PAHs detected in space would have
been formed "automatically", i.e., without any organismic intervention (!). Energy would have been
supplied to the process, probably via powerful bursts of radiation from many kinds of stellar and
similar sources.

Even more convincing evidence of the existence of PAHs in space and in other parts of the
universe is their presence in meteorites that have fallen to the earth. Extremely careful isolation of
carbon-containing substances from some meteorites has proved the presence of specific
polycyclic aromatic hydrocarbons.

Cyanide compounds, formed from the elements of carbon and nitrogen, have been shown by
spectroscopy to be prevalent in all comets, along with ice (spontaneously formed from hydrogen
and oxygen). All cyanides are considerably higher in energy content than carbon and hydrogen
and thus they must have been formed non-spontaneously thermodynamically.

In summary, there is ample evidence for the existence of complicated, orderly molecules in outer
space. They were formed without an organisms assistance because no such organisms have
been found associated with them in meteorites and, of course, none can thrive in the energetic
conditions of outer space. The "automatic" formation of complicated, orderly substances both
spontaneously and non-spontaneously is simply the consequence of normal chemical laws and
the second law of thermodynamics. (The intense energy sources in space make possible non-
spontaneous synthesis there.)

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The Essential Link Between Life and the Second Law of
Thermodynamics
The overall direction of change in the
universe is from less probable (more
organized) states to more probable (less
organized) states. Life does not "oppose" this
but rather makes use of it. The "downhill"
movement can be used to raise things
"uphill" (just as water flowing downhill
through a water wheel can be used to raise a
weight). There is, however, always a net loss
of organization in the process.

## For life on earth, the dissipation of energy

from the sun is the downhill movement.
Photosynthesis creates "uphill" molecules
which in turn can be used in cellular
molecules from which, in turn, all of the
"uphill" organization of life and culture
derive.

## All of biological and human organization

represents a state of improbability very much
less than that of the concentration of energy
in the sun, and one which would quickly
dissipate if the sun ceased shining (or there
was some disturbance in the chain of water
wheels which link the sun to biological and
cultural organization).

## Potential vs. Kinetic energy

Potential energy, as the name implies, is energy that has not yet been used, thus the term
potential. Kinetic energy is energy in use (or motion). A tank of gasoline has a certain potential
energy that is converted into kinetic energy by the engine. When the potential is used up, you're
outta gas! Batteries, when new or recharged, have a certain potential. When placed into a tape
recorder and played at loud volume (the only settings for such things), the potential in the
batteries is transformed into kinetic energy to drive the speakers. When the potential energy is
all used up, the batteries are dead. In the case of rechargeable batteries, their potential is
reelevated or restored.

In the hydrologic cycle, the sun is the ultimate source of energy, evaporating water (in a fashion
raising it's potential above water in the ocean). When the water falls as rain (or snow) it begins
to run downhill toward sea-level. As the water get closer to sea-level, it's potential energy is
decreased. Without the sun, the water would eventually still reach sea-level, but never be
evaporated to recharge the cycle.

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Chemicals may also be considered from a potential energy or kinetic energy standpoint. One
pound of sugar has a certain potential energy. If that pound of sugar is burned the energy is
released all at once. The energy released is kinetic energy (heat). So much is released that
organisms would burn up if all the energy was released at once. Organisms must release the
energy a little bit at a time.

Energy is defined as the ability to do work. Cells convert potential energy, usually in the from of
C-C covalent bonds or ATP molecules, into kinetic energy to accomplish cell division, growth,
biosynthesis, and active transport, among other things.

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