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Glossary:
Acid - an acid is a chemical that lowers the pH of a
solution. Acids
interact with other chemicals by donating hydrogen atoms or accepting
electrons.
Activation Energy - an energy barrier that must be crossed before
chemicals can react.
Actual Knowledge - the molecular knowledge contained in a gene or
protein.
Adenine - one of the bases in DNA and RNA. It is also one of the
components in ATP, ADP and AMP.
ADP - adenine diphosphate. ADP only has one high energy bond.
Alanine - hydrophobic amino acid.
Amino Acid - the building blocks of proteins. Life uses 20 amino acids
to build proteins. Amino acids have two sticky ends that can be joined
together to form long chains.
AMP - adenine monophosphate. AMP has no high energy bonds. It is
created in the cell from ATP when ATP is used to accomplish some
task that requires energy.
Arginine - a basic amino acid.
Aspartate - polar acidic amino acid.
Asparagine - charged amino acid.
ATP - adenine triphosphate. This is the energy source used by life. It
is made by plants during the process of photosynthesis. It is made by
animals as they digest food. ATP has 2 high energy bonds. Life knows
how to use the high energy bonds to do work.
ATP synthase - an enzyme that synthesizes ATP.
Axiom - a self evident assumption.
Base - a base is a term used in chemistry to describe a chemical that
raises the pH of a solution. Bases interact with other chemicals by
accepting hydrogen atoms or donating electrons.
Bit - a unit of information or knowledge.
Calculated knowledge - molecular knowledge calculated by the
methods outlined in chapter 4.
Carboxylic acid - one of the sticky ends on an amino acid.
Cell - the smallest living unit. Cells are surrounded by a membrane
which is composed of lipids and proteins. The chemicals inside cells
know how to grow and replicate. They accomplish this by using an
abundant energy to do useful work.
Chemical evolution - the hypothetical process by which the chemicals
necessary for life emerged on the primitive earth.
Chemical oscillators - a system of chemicals that change in a periodic
fashion with time. A wrist watch is a chemical oscillator.
Chromosome - very large continuous molecules of DNA.
Clustal - a computer program used to align amino acids in proteins.
Codon - a grouping of 3 bases in DNA or RNA that specifies a specific
amino acid in the final protein.
Common Ancestor - a animal, plant or bacteria whose descendants
evolved into two or more species.
Complexity - a non-repetitive pattern.
Condensation agent - a chemical that facilitates the formation of
chemical bonds between biological molecules by absorbing water.
Creation science - belief that the biblical account of creation is
scientifically accurate.
Cysteine - amino acid that can cross link peptide chains.
Cytosine - one of the bases used in DNA and RNA.
C-terminus - one of the sticky ends of an amino acid.
Darwinian evolution - evolution that involves small steps in
molecular knowledge. Naturalistic laws explain Darwinian evolution.
Deoxyribose - the sugar molecule found in DNA.
DNA - stands for deoxyribose nucleic acid. DNA is the molecule that
stores all of the knowledge that life needs to grow and replicate.
Sections of DNA that contain the knowledge to build proteins are
called genes.
Energy - the ability to do work.
Entropy - a measure of uncertainty.
Enzyme - a protein that catalyzes a chemical reaction.
280
Evolution by design - evolution that involves gigantic steps in
molecular knowledge. Naturalistic laws do not explain evolution by
design.
Evolution - the process through which existing knowledge is
optimized and preserved. While science relies of evolution to create
new knowledge, the probabilities associated with these events are too
remote.
Eukaryote - cells with a defined nucleus. Plants and animal cells are
composed of eukaryotic cells.
G3PD - an enzyme used by life to metabolize sugar.
Gene duplication - the process by which existing genes are
duplicated.
Gene - a section of DNA that contains the knowledge to build a
protein.
Genetic Code - the code that is used to build proteins from the
knowledge contained in DNA.
Glutamate - polar acidic amino acid.
Glutamine - polar charged amino acid.
Glycine - a small amino acid.
Guanine - one of the bases found in DNA and RNA.
Heat - the flow of energy from hot to cold objects.
Histidine - a basic amino acid.
Hydrophobic - a molecule that does not like water.
Knowledge - a useful reduction in uncertainty.
Leucine - hydrophobic amino acid.
Life - a system of chemicals possessing the molecular knowledge and
a mechanism to implement this knowledge in such a way to survive
long enough to replicate.
Lysine - a basic amino acid.
Infon - a step in molecular knowledge found by chance.
Information - a reduction in uncertainty. Information is not
necessarily useful.
Insulin - a protein that signals cells to take up sugar from the blood
stream.
Intelligent design - a methodology that relies on indirect logic to infer
the existence of a creator.
Investigator interference - process by which researchers alter the
results on their experiments.
Irreducible complexity - a system that requires two or more
components to function.
Isoleucine - hydrophobic amino acid.
Meteorites - rocks that fall from space and are recovered. Some
contain organic chemicals like amino acids.
Methionine - hydrophobic amino acid.
Micro-state - the arrangement of particles in a system.
Molecule - a chemical composed of two or more atoms.
Molecular Knowledge - the minimum amount of information
necessary to enable a chemical or group of chemicals to accomplish
some task or to specify some trait.
mRNA - stands for messenger ribonucleic acid. RNA is an
intermediate molecule involved in protein synthesis. Messenger RNA
transfers the knowledge to build proteins from the nucleus to the
ribosomes.
Natural selection - the process by which nature ensures that only
optimized genes are passed onto future generations. Natural selection
works against evolution because it does not allow existing genes to
evolve.
Naturalistic axiom - the assumption that everything can be explained
by physics, chemistry, biology and math.
N-terminus - one of the sticky ends of an amino acid.
Nucleotide - the building block for DNA and RNA. Each nucleoide
contains 1 phosphate, 1 ribose, and one of the 5 bases, adenine,
guanine, cytosine, thymine, or uracil.
Nucleus - the central compartment in eukaryotic cells. The nucleus
contains the DNA.
Peptide - a short chain of amino acids.
Perpetual motion machines - a machine that violates one or more of
the laws of physics.
Phenylanlanine - bulky amino acid.
Phosphodiester bond - the high energy bond between phosphate
groups in ATP.
Polar - a molecule that likes water.
Poly-nucleotide - a string of nucleotides.
Pre-RNA - hypothesized molecule that proceeded RNA during
chemical evolution.
Primordial soup - the hypothetical small pond in which life
originated.
Prokaryote - cells without a defined nucleus. Bacteria cells are
prokaryotic cells.
Proline - unusual amino acid that introduces a kink into a protein
chain.
Protein - a chemical composed of amino acids that is used by life to
implement the molecular knowledge found in genes.
Protein databank - an online Database that contains the 3-D structure
of many proteins.
Protein domain - a section of a protein that performs some function
or specifies some 3-D shape.
Protein family - a group of related proteins with similar 3-D structures
and amino acid sequences.
Proteinoids - long branched chains of amino acids formed by heating.
Observable axiom - the assumption that man is capable or accurately
observing the world around him.
Order - a repetitive pattern.
Oxidation - a chemical reaction in which electrons are transferred
from one atom to another.
Quantum mechanics - the physics that describes small particles.
Rasmol - a free computer program that allows users to view
molecules like proteins and DNA.
Relative entropy - a measure of uncertainty.
Ribose - the sugar molecule found in RNA.
Ribozyme -an RNA molecule that also functions as an enzyme.
Ribosome - a complex of RNA and proteins. Proteins are built by the
process of translation at ribosomes.
RNA - RNA contains molecular knowledge and can sometimes
implement molecular knowledge. Messenger RNA (mRNA), transfer
RNA (tRNA), and ribosomal RNA (rRNA) help cells use the
knowledge contained in DNA to build proteins.
Second law of thermodynamics - states that the entropy of the
universe increases with time. This happens because particles always try
to find their most probable distribution. This is the distribution that
maximizes the number of available micro-states.
Serine - a polar amino acid.
Science - a methodology that relies on the observable and naturalistic
axioms to design and interpret scientific experiments.
Shannon entropy - the average uncertainty per symbol.
Species - a group of interbreeding animals.
Specified Complexity - any outcome that is not ordered and is
predicted in advance.
Swiss Prot - an online Database that contains the amino acid sequence
of most proteins.
Thermal proteins - long branched chains of amino acids formed by
heating.
Thermodynamics - the field of physics that deals with heat, energy
and work. Chemical thermodynamics is a subset of this discipline that
deals with chemicals and how they interact.
Threonine - a polar amino acid.
Transcription - the process that writes DNA into mRNA.
Translation - the process that uses mRNA to create proteins.
Thymine - one of the bases found in DNA.
tRNA - stands for transfer ribonucleic acid. Transfer RNA brings
amino acids to ribosomes for protein synthesis.
Tyrosine - bulky amino acid.
Tryptophan - bulky amino acid.
Uracil - one of the bases found in RNA.
Valine - hydrophobic amino acid.
This book would not have been possible without
numerous online
programs and resources.
The Protein Database:
www.Pdbbeta.rcsb.org The protein database that houses the 3-D
structure of many proteins. These can be viewed online with interactive
programs that allows users to zoom in and rotate the structures.
Rasmol:
www.umass.edu/microbio/rasmol/distrib/rasman.htm Displays 3-D
structures of proteins in the protein database. Used to create most of
the pictures inside this book and on the cover.
Swiss Prot:
www.us.expasy.org/sprot/ Contains the amino acid sequence of most
proteins.
Consurf:
www.consurf.tau.ac.il/ Colors 3-D displays by amino acid
conservation. Generates a script to apply in rasmol. This program was
used to color the amino acids on the back cover.
Glaser F./ Pupko T., Paz I., Bell R.E., Becher D., Martz E., Ben-
Tal N., Consurf: Identification of Functional Regions in Proteins by
Surface Mapping of Phylogentic Information, Bioinformatics, Vol. 19,
no, 1, 2003 pp163-164.
Clustal:
http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html An easy to
use windows interface for the Clustal alignment program. This
program was used in chapter 4 to align insulin in several different
species and again in chapter 14 for G3PD.
Subject Index:
Activation Energy 123-124,
130-133
Activated Nucleotides 173
Adenine Synthesis 205,297
Amino Acids 149-155
ATP 94, 217, 223
Synthesis 234-236
Calculated Molecular
Knowledge 83
Cambrian Explosion 14
Chemical Bonds 108-109
Chemical Equilibrium 124
Chemical Evolution 8
Chemical Kinetics 122
Chemical Oscillators 139-140
Common Ancestor 214-216
Complexity 31
Condensation Agents 167, 171
Creation Science 15
Cytosine 169
Dawkins 7
Darwin 35
Darwinian Evolution 36
DNA 46-47, 142-144
Replication 47-48
Energy 8, 111
Enzymes 129-135
Evolution by Design 36
Evolution of Knowledge 93
Eukaryotes 60
Gene Duplication 3, 258, 263- 265
Genetic Code 49
Information 17, 18, 19, 24, 25, 31, 38-39
Infon 29
Insulin (information and
Knowledge) 63-85
Investigator Interference 161,
174-177
Irreducible Complexity 200-
202
Matter 111
Meteorites 90
Micro-states 114-120
Miller’s Experiment 162-163
Molecular Knowledge 4, 5, 11, 18, 28-39, 83, 101, 102,
212-214, 226-232
Molecular Information 4
Molecular Theory of Evolution 2
Mutation 2, 49
Natural Selection 4,5 250-254
Naturalistic Axiom 1, 267
Non-equilibrium
Thermodynamics 137
Observable Axiom 267
Open Systems 127
Order 31
Origin of Life 10, 214, 248
Oxidation 220-222
Peptides
Short 165
Long 166
Perpetual Motion 12, 191, 194,286
Prebiotic Synthesis
Nucleotides168-170
Pre-RNA 171
Primordial Soup 8, 95-97, 196
Prokaryotes 60
Proteins
First 92, 98
Structure 57-59
Translation 40-41, 52-56
Thermal 164
Self Replication 181-183
Proton Gradient 222
Punctuated Equilibrium 255
Quantum Mechanics 112-116
Relative Entropy 272
RNA 144-147
Self Replication 10,12,13
184-195
Second Law 116, 117, 118, 129-136
Shannon Entropy 27, 270-271
Specified Complexity 32
Tree of Life 205, 218
Time 239, 244, 247
Author Index:
Bartel 187-188
Behe 200-202, 264
Brillouin 27
Crick 2
Dawkins 7
Darwin 2, 35-37, 85, 252
Dembski 31-32
Ferris 8
Fox 9, 164
Joyce 8, 185-186
Lee 181
Mayr 215
Meyer 14
Miller 8, 162-163
Ohno 3
Orgel 8, 11,185-186
Shapiro 8, 169-170
Thaxton 8, 161, 169-170
Watson 2
Woese 214-215, 287
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