Bacterial Physiology and Biochemistry

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 BACTERIAL
PHYSIOLOGY AND BIOCHEMISTRY
This page intentionally left blank
 Progress in Biochemistry and Biotechnology

BACTERIAL
PHYSIOLOGY AND BIOCHEMISTRY

Ivan Kushkevych
Department of Experimental Biology,
Faculty of Science, Masaryk University,
Brno, Czech Republic

Edited by
Josef Jampílek
Academic Press is an imprint of Elsevier
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Publisher (other than as may be noted herein).

Notices
Knowledge and best practice in this field are constantly changing. As new research and
experience broaden our understanding, changes in research methods, professional practices, or
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Practitioners and researchers must always rely on their own experience and knowledge in
evaluating and using any information, methods, compounds, or experiments described herein.
In using such information or methods they should be mindful of their own safety and the safety
of others, including parties for whom they have a professional responsibility.

To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors,
assume any liability for any injury and/or damage to persons or property as a matter of products
liability, negligence or otherwise, or from any use or operation of any methods, products,
instructions, or ideas contained in the material herein.

ISBN: 978-0-443-18738-4

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Cover Designer: Matthew Limbert

Cover input from Igor Starunko

Typeset by STRAIVE, India
 CONTENTS

ACKNOWLEDGEMENTS...................................................................................................... ix

ABBREVIATIONS.................................................................................................................. xi

FOREWORD.......................................................................................................................... xiii

CHAPTER 1. INTRODUCTION INTO BACTERIAL PHYSIOLOGY

AND BIOCHEMISTRY .................................................................................... 1
1.1. Subject of study ........................................................................................ 1
1.2. Bacteria in the phylogeny of living organisms
and diversity of cell shapes ...................................................................... 3
1.3. Bacterial evolution ...................................................................................7
1.4. Methods of studies of bacterial properties ............................................. 11

CHAPTER 2. BACTERIAL CHEMICAL COMPOSITION AND FUNCTIONAL

CELL STRUCTURES ..................................................................................... 23
2.1. Elemental composition ...........................................................................23
2.2. Compounds composition .......................................................................24
2.3. Bacterial nucleus .................................................................................... 33
2.4. Cytoplasm ...............................................................................................36
2.5. Plasma membrane ..................................................................................44
2.6. Cell wall .................................................................................................50
2.7. Flagella, pilus, and fimbria ..................................................................... 64
2.8. Bacterial capsule ....................................................................................72
2.9. Endospores .............................................................................................77
2.10. Pigments ................................................................................................. 85

CHAPTER 3. BACTERIAL NUTRITION AND GROWTH................................................. 91

3.1. Basic sources of nutrition........................................................................91
3.2. Sources of carbon.................................................................................... 92
3.3. Sources of nitrogen.................................................................................. 94
3.4. Mineral nutrition.....................................................................................95
3.5. Growth factors......................................................................................... 98
v
contents
3.6. Sources of energy.................................................................................. 108
3.7. Transport of compounds across the plasma membrane......................... 110
3.8. Passive transport.................................................................................... 111
3.9. Active transport.....................................................................................112
3.10. Transport of iron and its regulation.......................................................116
3.11. Transport of proteins ............................................................................124
3.12. Group translocation...............................................................................126
3.13. Bacterial growth and multiplication .....................................................127
3.13.1. Growth under conditions of static cultivation.......................... 130
3.13.2. Growth constants...................................................................... 133
3.13.3. Deviations from normal growth curve..................................... 136
3.14. Multiplication of microorganisms under conditions
of continuous (dynamic) cultivation......................................................138
3.15. Synchronous multiplication . ................................................................ 145
3.16. Bacterial cell cycle................................................................................ 146

CHAPTER 4. PROCESSES OF CELL DIFFERENTIATION.............................................. 151

4.1. Characteristics of differentiation processes........................................... 151
4.2. Polar differentiation in species of Caulobacter genus........................... 153
4.3. Differentiation of photosynthetic membranes
in facultative phototrophic bacteria....................................................... 156
4.4. Formation of heterocyst in cyanobacteria
under bound nitrogen deficiency........................................................... 157 t

CHAPTER 5. BACTERIAL METABOLISM....................................................................... 159

5.1. Energy of biochemical reactions........................................................... 160
5.2. Carriers of hydrogen.............................................................................. 163
5.3. Role of ATP and its formation in bacterial cells.................................... 166
5.4. Types of phosphorylation ..................................................................... 173
5.5. Processes of catabolism.........................................................................176
5.5.1. Catabolism of carbon compounds and fermentation..................177
5.5.1.1. Ethanol fermentation...................................................179
5.5.1.2. Lactic acid fermentation.............................................183
5.5.1.3. Pentose sugars fermentation....................................... 185
5.5.1.4. Propionic acid fermentation pathway......................... 188
5.5.1.5. Butyric acid fermentation and solvent formation....... 190
5.5.1.6. Mixed acid fermentation pathway.............................. 195
5.5.1.7. Fermentation of sugars and polysaccharides..............198

vi
 contents
5.5.2. Anaerobic respiration................................................................. 199
5.5.2.1. Nitrate reduction and denitrification...........................199
5.5.2.2. Sulfate reduction (desulfurization)............................. 202
5.5.2.3. Carbon (IV) oxide reduction to methane....................208
5.5.3. Aerobic respiration in chemolithotrophic bacteria..................... 210
5.5.3.1. Oxidation of ammonia................................................ 211
5.5.3.2. Oxidation of reduced sulfur compounds..................... 213
5.5.3.3. Oxidation of iron compounds.....................................216
5.5.3.4. Oxidation of hydrogen................................................217
5.5.3.5. Oxidation of methane.................................................. 218
5.5.4. Aerobic respiration in chemoorganotrophic bacteria................. 218
5.5.4.1. Incomplete oxidation of substrate...............................219
5.5.4.2. Complete oxidation of substrate.................................220
5.5.4.3. Oxidation of saccharides and polysaccharides...........225
5.5.4.4. Oxidation of lipids......................................................227
5.5.4.5. Oxidation of hydrocarbons.........................................229
5.5.5. Catabolism of nitrogenous compounds...................................... 233
5.5.5.1. Dissimilation of proteins and amino acids.................. 233
5.5.5.1.1. Anaerobic degradation
(amino acid fermentation).......................... 233
5.5.5.1.2. Aerobic (oxidative) catabolism
of amino acids............................................240
5.5.6. Catabolism of heterocyclic compounds..................................... 246
5.5.6.1. Fermentation of heterocyclic compounds................... 246
5.5.6.2. Oxidation of heterocyclic compounds........................249
5.6. Processes of anabolism (biosynthesis)..................................................251
5.6.1. Biosynthesis of saccharides....................................................... 251
5.6.2. Biosynthesis of lipids.................................................................259
5.6.3. Consumption of CO2 by heterotrophic bacteria.........................265
5.6.4. Fixation of molecular nitrogen...................................................268
5.6.5. Biosynthesis of amino acids.......................................................269
5.6.6. Biosynthesis of nucleotides........................................................278
5.6.7. Biosynthesis of nucleic acids..................................................... 282
5.6.8. Biosynthesis of proteins.............................................................285
5.7. Regulation of metabolism process........................................................291
5.7.1. Regulation of enzyme synthesis................................................. 292
5.7.2. Regulation of enzymatic activity...............................................297
5.7.3. Specifics of regulation mechanisms...........................................298
5.7.4. Regulation of energetic metabolism...........................................300
vii
contents
5.8. Metabolism of phototrophic bacteria.................................................... 301
5.8.1. Photolithotrophs......................................................................... 301
5.8.2. Photoorganotrophs..................................................................... 305

CHAPTER 6. GROWTH OF MICROORGANISMS IN NATURE ....................................311

6.1. Microorganisms as part of the ecosystem............................................. 311
6.2. Physiological role of microorganisms in ecosystems............................ 313
6.3. Intercellular and internal population interactions
and quorum-sensing regulation of gene expression..............................315
6.4. Luminescent bacteria and bioluminescence.......................................... 319

CHAPTER 7. EFFECT OF ENVIRONMENTAL FACTORS

ON BACTERIAL CELLS.............................................................................. 325
7.1. Effect of external factors on bacteria.....................................................325
7.2. Mechanisms of the effect of environmental factors..............................328
7.2.1. Physical factors..........................................................................328
7.2.2. Chemical factors........................................................................ 335
7.2.3. Chemotherapeutics..................................................................... 345
7.3. Antibiotics and their mechanisms of action..........................................348
7.3.1. Antibiotics inhibiting cell wall synthesis................................... 348
7.3.2. Antibiotics disrupting the plasma membrane.............................353
7.3.3. Antibiotics disturbing the metabolism of nucleic acids............. 354
7.3.4. Antibiotics inhibiting protein synthesis..................................... 355
7.3.5. Antibiotics affecting phosphorylation process...........................358

RECOMMENDED REFERENCES.......................................................................................361

INDEX ...................................................................................................................................363

viii
 ACKNOWLEDGEMENTS

Scientific reviewers:
Prof. PharmDr. Josef Jampílek, Ph.D., Professor of Medicinal Chemistry, Department of Chemical Biology,
Faculty of Science, Palacky University Olomouc, Slechtitelu 27, 783 71 Olomouc, Czech Republic;
Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava,
Ilkovicova 6, 842 15 Bratislava, Slovakia
Prof. Lorenzo Drago, Ph.D., Professor of Clinical Microbiology, Department of Biomedical Sciences for
Health, University of Milan, 20133 Milan, Italy
Prof. Aidan Coffey, Ph.D., Professor of Microbiology, Department of Biological Sciences, Cork Institute
of Technology, Bishopstown, Cork, Ireland

This educational book contains the modern knowledge of bacterial physiology and biochemistry.
The book includes seven chapters that describe the subject of bacterial physiology, chemical composition,
functional cell structures, nutrition, growth, and the processes of cell differentiation. Special attention
is paid to the bacterial metabolism, including the processes of catabolism and anabolism. The energy
of biochemical reactions, carriers of hydrogen, the role of ATP in the bacterial cells, and types of
phosphorylation are also discussed. The physiological role of bacteria in ecosystems, intercellular and
internal population interactions, quorum-sensing regulation of gene expression, and luminescent bacteria
and bioluminescence are described. The effect of environmental factors on bacteria, including physical
and chemical factors, and their mechanisms are presented. The description of chemotherapeutics and
antibiotics and mechanisms of their action is also provided. This book can be helpful for bachelor and
master students who study General Microbiology, Medical Microbiology, Veterinary Microbiology, and
Molecular Biology, for microbiologists, biochemists, biologists, experts in the cell and molecular biology,
and for readers interested in the study of bacterial physiology and biochemistry.

Acknowledgments: The author sincerely thanks Igor Starunko from Ivan Franko National Univer-
sity of Lviv (Ukraine) for his help and the technical preparation of the illustrative material and layout of
the book. The author also expresses special thanks to the scientific editor, Prof. Josef Jampílek, as well as
the reviewers, Prof. Lorenzo Drago and Prof. Aidan Coffey, for their time and help, critical comments,
and recommendations during preparation of this book.
Ivan Kushkevych

ix
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 chapter 1. introduction into bacterial physiology and biochemistry

ABBREVIATIONS

ATP Adenosine triphosphate

Abe Abequose
ADP Adenosine diphosphate
AMP Adenosine monophosphate
APS Adenosine-5′-phosphosulfate
BChl Bacteriochlorophylls
BLAST Basic local alignment search tool
CAP Catabolite activator protein
Chl Chlorophylls
CTP Cytidine triphosphate
Cyt Cytochrome
Da Daltons
DAP Diaminopimelic acid
dATP Deoxyadenosine triphosphate
dCTP Deoxycytidine triphosphate
dGTP Deoxyguanosine triphosphate
DHB 2,3-Dihydroxybenzoate
DNA Deoxyribonucleic acid
dTTP Deoxythymidine triphosphate
dXDP Deoxyribonucleotide diphosphate
EDP Entner–Doudoroff pathway
EDTA Ethylenediaminetetraacetic acid
EMBL European Molecular Biology Laboratory
EMP Embden–Meyerhof–Parnas pathway
FA Fatty acids
FACS Fluorescence activated cell sorting
FAD Flavin adenine dinucleotide
Fd Ferredoxin
Feb Ferrienterochelin-binding protein
FMN Flavin mononucleotide
Gal Galactose
GDP Guanosine diphosphate
Glu Glucose
GluN Glucosamine
GSB Green sulfur bacteria
GSH Reduced glutathione
GSSG Oxidized glutathione
xi
abbreviations
GTP Guanosine triphosphate
GTP Guanine triphosphate
Hase Hydrogenase
HDHD 3-Hydroxydecanoyl-3-hydroxydecanic acid
Hep Heptose
HM Hydroxy muramic acid
HMP Hexose-monophosphate pathway
HPLC High-performance liquid chromatography
KDO 2-Keto-3-deoxy-octonoic acid
KEGG Kyoto Encyclopedia of Genes and Genomes
LPS Lipopolysaccharide
LTPP Lipothiamine pyrophosphate
Man Mannose
MR-test Methyl red test
NAD Nicotinamide adenine dinucleotide
NAG N-Acetylglucosamine
NAM N-Acetylmuramic acid
NRPS Nonribosomal peptide synthetases
OAc O-acetyl
ORF Open reading frame
PAPS 3′-Phosphoadenosine-5′-phosphosulfate
PAS 4-Aminosalicylic acid
PCR Polymerase chain reaction
PEP Phosphoenolpyruvate
QS Quorum-sensing
Rha Rhamnose
RNA Ribonucleic acid
SDS Sodium dodecyl sulfate
TCA Tricarboxylic acid
TDP-rha Thymidine diphosphate rhamnose
THF Tetrahydrofolic acid
TPP Thiamine pyrophosphate
UMP Uridine monophosphate
UTP Uridine triphosphate
UV Ultraviolet
VP-test Voges–Proskauer test
XDP Ribonucleotide diphosphate

xii
FOREWORD

All things are hidden, obscure and debatable if the cause

of the phenomena is unknown, but everything is clear if its cause be known.
Louis Pasteur

B acterial Physiology and Biochemistry is an educational book designed for

use in advanced bachelor’s and master’s courses in biology, including micro-
biology, biochemistry, and molecular biology. This book contains curriculum taught to
biology students specializing in microbiology. The knowledge of this subject is required
within the above-mentioned specialization in partial and state exams. The content of the
text and the way of organization are based on the relevant microbiology curriculum, cor-
responding to the requirements of the new educational system at the faculties of science.
The necessary knowledge of biochemistry and organic chemistry and mastering the
basics of general microbiology are assumed. In a clear form defined by the relevant cur-
riculum, the text can also be used to prepare students of professional and teacher biology
for the partial exam in the physiological part of general microbiology. This book pro-
vides the most current, authoritative, and relevant presentation of bacterial physiology
and biochemistry and includes seven chapters about the subject of the book in general,
bacterial chemical composition and functional cell structure, nutrition and growth, pro-
cesses of cell differentiation, metabolism, and the influence of environmental factors.
The first chapter describes the subject of bacterial physiology and biochemistry,
bacteria in the phylogeny of living organisms and their shape diversity and evolution.
This chapter also presents methods for studying bacterial properties. Detailed informa-
tion on the chemical composition and functional cell structure of bacteria is described in
the second chapter. It includes the element and compound composition, and characteri-
zes the bacterial nucleus, cytoplasm, plasma membrane, cell wall, flagella, pilus and
fimbriae, bacterial capsule, endospores, and pigments.
An integral part of bacterial physiology is microbial nutrition and growth as well
as basic sources of nutrition, including sources of carbon and nitrogen. Therefore, the
third chapter of this book presents mineral nutrition, growth factors, energy sources,
and transport of substances across the plasma membrane. Furthermore, the growth and
multiplication of bacteria, their growth under static culture conditions, growth constants,
and deviations from the normal growth curve are described. This important chapter con-
cludes with the multiplication of bacterial populations under conditions of continuous
(dynamic) cultivation, synchronous multiplication, and the bacterial cell cycle.
The text of the fourth chapter presents the process of cell differentiation, characteris­
tics of differentiation processes, polar differentiation, differentiation of photosynthetic
membranes in facultative phototrophic bacteria, and the formation of heterocysts in
cyanobacteria under bound nitrogen deficiency.
xiii
foreword
Special attention is paid to bacterial metabolism, energy of biochemical reactions,
hydrogen carriers, the role of ATP in cells, and types of phosphorylation. The chapter
describing metabolic processes is divided according to two metabolic pathways into
catabolism and anabolism sections. The processes of catabolism of carbon compounds
and fermentation of ethanol, lactic acid, pentose sugars, propionic acid, butyric acid
with solvent formation, mixed acids, and sugars and the fermentation pathway of poly-
saccharides are described in detail. Then anaerobic respiration is shown, including
nitrate reduction and denitrification, sulfate reduction, and reduction of carbon dioxide
to methane. The process of aerobic respiration in chemolithotrophic bacteria, including
oxidation of ammonia, reduced sulfur and iron compounds, hydrogen, and methane, is
represented in sections of this chapter. Aerobic respiration in chemoorganotrophic bac-
teria is also described, especially incomplete oxidation of alcohols and glucose as well
as complete oxidation of substrates. Nitrogen catabolism, protein, and amino acid dis-
similation are characterized. Anaerobic degradation and aerobic metabolism of amino
acids and heterocyclic compounds as well as fermentation and oxidation of heterocyclic
compounds complete the section about bacterial catabolism. Special attention is paid
to the processes of anabolism, including carbohydrate and lipid biosynthesis, carbon
dioxide consumption by heterotrophs, and molecular nitrogen fixation. The biosynthesis
of amino acids, nucleotides, nucleic acids, and proteins is shown. In addition, the regula-
tion of the metabolic process and the metabolism of phototrophic bacteria are summa-
rized in this chapter, which is one of the largest chapters of the book.
Physiological and biochemical processes depend on the environment. Therefore,
the next chapter characterizes microbial growth in nature, bacterial populations as part
of the ecosystem, and their physiological role in ecosystems. In addition, intercellu-
lar and internal population interactions, quorum-sensing regulation of gene expression,
luminescent bacteria, and bioluminescence are presented. The last chapter of this book
describes the influence of environmental factors on bacteria, including physical and
chemical factors, and chemotherapeutics. Antibiotics and their mechanisms of action are
also demonstrated. This book concludes with the description of antibiotics that inhibit
cell wall synthesis, disrupt the plasma membrane, and affect nucleic acid metabolism,
protein synthesis, and the phosphorylation process.

Prof. Lorenzo Drago, Ph.D.,

Professor of Clinical Microbiology,
Department of Biomedical Sciences for Health,
Faculty of Medicine and Surgery at University of Milan, Italy

xiv
 chapter 1. introduction into bacterial physiology and biochemistry

CHAPTER 1

INTRODUCTION INTO BACTERIAL

PHYSIOLOGY AND BIOCHEMISTRY

I n this chapter, the studies of bacterial physiology and biochemistry and their
main goals are characterized. Bacteria in the phylogeny of living organisms and
diversity of cell shapes are described. Special attention is paid to the comparison of
cell structures and their metabolic properties in different organisms, including bacteria,
archaea, and eukaryotes. Moreover, main features of bacterial evolution and methods
of modern bacterial physiology and biochemistry are presented.

1.1. Subject of study

The subject of bacterial physiology is the study of the functions of bacterial cells,
that is, the study of all physical, chemical, and biological processes occurring in the cell
as well as physical, chemical, and biological transformations caused by bacteria in the
environment during their development. Such studies are impossible without familia­
rizing with the organization of morphology and functional structures of the microbial
cell. For performing biological functions, bacterial cells are differentiated into architec-
tural and functional structures.
An important part of bacterial physiology is the study of the chemical composi-
tion of bacterial cells, which, albeit similar to the chemical composition of the cells of
higher organisms, has certain peculiarities. These features are related to the ability of
bacteria to adapt to the environment. Due to such adaptation, depending on the environ-
ment, different variants of the same microorganism by morphological and physiological
characteristics can be observed. The process of adaptation is explained not only by the
existence of various types of bacterial metabolism, but also by the transformation of
the saprophytic state into parasitic and the appearance of pathogenic microorganisms.
The following two types of living organisms are distinguished by the cell structure:
ƒƒprokaryotic cells (bacterial and archaeal cells that do not have a formed
nucleus);
ƒƒ eukaryotic (cells with the nucleus).
Bacterial Physiology and Biochemistry 1
http://doi.org/10.1016/B978-0-443-18738-4.50001-2,
Copyright © 2023 Elsevier Inc. All rights reserved.
bacterial physiology and biochemistry

Prokaryotic and eukaryotic cells differ in structural organization. Prokaryotes,

unlike eukaryotes, do not have membrane-bound compartments called organelles that
perform specialized functions. As mentioned above, prokaryotic cells do not have
a formed nucleus, and hereditary information (DNA) in prokaryotes is not separated
from other components of the cell. This feature is the most important difference
between prokaryotic and eukaryotic cells. A comparison of the cellular structure of
eukaryotic and prokaryotic cells is presented in Table 1.1.

Table 1.1. Comparison of bacteria, archaea, and eukaryotes

Properties Bacteria Archaea Eukaryotes

Nucleus with a nuclear membrane

Absent Absent Present
around the DNA

Complex of internal membrane

Absent Absent Present
organelles

Have peptidoglycan, Do not have Do not have

Cell wall
muramic acid muramic acid muramic acid

Esterified, Esterified, branched, Esterified,

Membrane lipids
not branched aliphatic chains not branched

Gas vesicles Present Present Absent

Contains thymine, Does not contain Contains thymine,

RNA transfer
N-formylmethionine thymine N-formylmethionine

Polycistronic mRNA Present Present Absent

Introns of the mRNA Absent Absent Present

Splicing of the mRNA Absent Absent Present

Ribosomes:
Size 70S 70S 80S
Sensitivity to chloramphenicol and Positive Negative Negative
kanamycin

DNA-dependent RNA polymerase

Number of enzymes One Few Three
Structure Simple subunit Complicated Complicated
(4 subunits) Subordinate structure Subordinate structure
(8–12 subunits) (12–14 subunits)
Sensitivity to rifampicin Positive Negative Negative

Polymerase II promoters Absent Present Present

Metabolism:
Similar ATPase Absent Present Present
Methanogenesis Absent Present Absent
Fixation of nitrogen Present Present Absent
Photosynthesis with participation
of chlorophyll Present Absent Present
Chemolithotrophs Present Present Absent

2
 chapter 1. introduction into bacterial physiology and biochemistry

The comparison of similar properties of organisms, regardless of the presence of

the nucleus, is presented in Fig. 1.1.

Contain molecules that transmit Capable of grown and

Age highly organized
hereditary information reproduction

Cells of all organisms, regardless of the presence of the nucleus,

have the similar properties

Have a cellular metabolism, in which

Express hereditary information
energy is used and they convert
in transcription and translation processes
the compounds into cellular structures

Fig. 1.1. Comparison of similar properties of organisms.

Thus, prokaryotic and eukaryotic cells differ in structural organization, although

the cells of all organisms, regardless of the presence of the nucleus, have similar
properties. So, bacterial physiology studies the chemical composition of bacterial
cells, physical and biological processes occurring in the cells, and transformations of
different metabolic compounds.

1.2. Bacteria in the phylogeny of living organisms

and diversity of cell shapes
Microbiology is a branch of science that covers the study of viruses, archaea,
bacteria, fungi, algae, and protozoa. There are no significant differences in the intracel-
lular structure of bacteria and archaea. There are fundamental biochemical differences
between them, which reflects their evolutionary origin. About 10 years ago, most sci-
entists believed that evolution was in two ways: one of them led to the formation of
prokaryotic cells (bacteria), and the other to the emergence of eukaryotic cells. The
terms “bacteria” and “prokaryotes” were considered synonymous. These views have
undergone radical changes in the 80s of the last century, when Carl Richard Woese,
a molecular biologist, began analyzing information molecules that directly reflect
hereditary cell information.
The analysis of ribosomal RNA showed that there are three principal lines of evo-
lution that form three separate domains of cell evolution:
ƒƒ bacterial cells;
ƒƒrchaeal cells;
ƒƒ eukaryotic cells (mushroom, algae, protozoa, plants, animals).
3
bacterial physiology and biochemistry

The conducted studies allowed determining:

•• organelles of eukaryotes;
•• cells involved in the formation of energy (mitochondria and chloroplasts) come
from prokaryotic cells that have lost their ability to live independently;
•• organisms evolved in three different ways from one common predecessor, which
led to the formation of a large variety of microorganisms, plants, and animals
that exist today.
Due to the received information, a new system of classification of living orga­
nisms was created. It is based on the analysis of rRNA macromolecules.
It is assumed that there was a certain common ancestor “progenote,” which gave
rise to the three branches of the evolutionary tree (Fig. 1.2). How it was, it is unknown.

Bacteria Archaea Eukaryota

Green Slime molds
filamentous bacteria
Spirochetes Entamoebae Animals
Gram Fungi
Methanosarcina
positives Methanobacterium Halophiles
Plants
Proteobacteria Methanococcus
Thermococcus celer Ciliates
Cyanobacteria
Thermoproteus Flagellates
Planctomyces Pyrodictium
Trichomonads
Bacteroides
Cytophaga Microsporidia

Thermotoga Diplomonads

Aquifex

Fig. 1.2. Phylogenetic tree of life by Carl Woese et al. (1990).

Archaea are highly specialized prokaryotic organisms, and although they are simi-
lar to bacteria in the structural organization, they have a number of fundamental diffe­
rences. The most important feature of the archaea is the specificity of their ribosomal
and transport RNA; their ribosomes differ in shape. Differences were also found in
other components of the protein synthesis system. Archaea do not have fatty acids and
polyhydric alcohols as part of membrane lipids and usually have from 20 to 40 carbon
atoms. The lipid layer of the membrane is formed by a monomolecular layer, which,
obviously, gives its strength. Externally, archaea often have surface layers formed in
a certain way by structured and regularly packed protein or glycoprotein molecules of
the correct and sometimes strange form. The structure of the cell wall of the archaea may
include peptides and polysaccharides. Some archaea are characterized by processes that
are not intrinsic to other organisms. For example, some representatives of this group
of prokaryotes form methane (methanogens) in their process of life. Most archaeas are
extremophiles, that is, they develop under extreme conditions, at high temperatures
(+90 °C) or in saturated saline solutions. Acidophilic archaea grow in the environment,
4
 chapter 1. introduction into bacterial physiology and biochemistry

where the pH is as low as in the concentrated sulfuric acid. There are autotrophic forms
of archaea that do not require organic food but are satisfied with the energy obtained
through oxidation–reduction reactions, with the involvement of inorganic molecules.
Bacteria that differ in their morphological and physiological properties are an
extremely diverse group of prokaryotic microorganisms. They can be spherical, cylin-
drical, spiral, and pleomorphic (Fig. 1.3).

Spherical (cocci) Rods (bacillus)

Micrococcus
Plane of
division Single bacillus
Diplococci

Diplobacilli

Streptococci

Streptobacilli
Tetrad

Sarcina
Coccobacilli

Staphylococci
Spiral shapes

Vibrio Spirillum Spirochete

Fig. 1.3. Basic shapes of bacterial cells: spherical (coccus, cocci), rods (bacteria, bacillus), and spirals.

5
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qualifications of a popular teacher. He would not have aspired to
finished eloquence of style: to the eloquence of gesture and of
manner, he was still more a stranger. But there is an eloquence of
physiognomy, which Mr. Rittenhouse most eminently possessed.
The modesty and amenity of his manner would have effected much,
whether his audience had been a class of philosophers, or an
assembly of ladies. Of his own discoveries, and opinions, and
theories, he would have always spoken with that sweet and modest
reserve, for which he was ever distinguished. He would have dwelt
with the most generous and ample enthusiasm upon the great
discoveries of Newton; and if, at any time, he could have forgotten
that impartial conduct, which it is the duty of the historian of a
science to observe, it would have been when he might have had
occasion to defend the theories of that great man, against the
objections of succeeding and minor philosophers.

In Physics, Newton was his favourite author. Of HIM he ever spoke

with a species of respect bordering upon veneration. He considered
him as one of those few great leaders in science whose discoveries
and services can never be forgotten: whose fame, instead of
diminishing, is destined to be augmented, with the progress of time. I
had many opportunities of being witness to the exalted opinion which
he entertained of the immortal British philosopher. He read Dr.
Bancroft’s objections to some parts of Sir Isaac’s theory of colours,
with a firm conviction, that the Newtonian principles were still
unshaken: and I well remember, that he once referred me to a paper
which he had published, in one of our magazines, in answer to some
objections which the late Dr. Witherspoon had urged against some of
the theories of Newton.

It has been observed by a celebrated writer, that mathematicians

in general read but little of each other’s works. This remark, if I
mistake not, is very strongly illustrated in Mr. Rittenhouse. However it
may have been in his earlier age, I am confident that during the last
thirteen years of his life, when my intercourse with him was great,
and indeed but little interrupted; I am confident, that at this matured
and auspicious era of his life, our friend was not a laborious student.
He looked into many books, and he often passed quickly from one
kind of reading to another: from philosophy to poetry; from poetry
perhaps to philosophy again. His reading may be said to have been
desultory. I have little doubt that this rather irregular manner of
reading was, in some measure, the result of his extreme delicacy of
constitution, which rendered a more unvaried application to any one
kind of reading, irksome and oppressive. Often have I seen him lay
down his book or pen, to recline upon his sopha, the circumscribed
flush upon his cheeks plainly indicating the physical state of his
feelings. A short repose would enable him to return to his studies
again.

Mr. Rittenhouse’s application to books, had, no doubt, been more

regular and constant in the earlier part of his life; before I knew him
well, or before I had accustomed myself to watch the progress of his
mind. He was, certainly, profoundly, acquainted with the Principia
and other writings of Newton, which he read partly in the original,
and partly through the medium of translation. And although, within
the period of my better acquaintance with him, his reading I have
said, was not intense, he suffered no important discovery in
philosophy to escape his notice. Although his own library was small,
he had ample opportunities, through the medium of the valuable
library belonging to the Philosophical Society, and other collections
in Philadelphia, of observing the progress of his favourite studies in
Europe. He took much interest in the discoveries of Mr. Herschel,
whose papers he eagerly read as they arrived from Europe: and I
well remember the time (in 1785) when he was engaged in reading
Scheel’s work on Fire, which had recently appeared, in an English
dress. He then assured me, that some of this great Swedish
philosopher’s notions concerning the nature and the laws of heat,
had long before suggested themselves to his mind.

The chemical discoveries of Crawford and Priestley solicited some

of Mr. Rittenhouse’s attention, about the year 1785-1786, and for
some time after. The brilliant discoveries of Priestley, in particular,
were not unknown to him. Upon the arrival of this illustrious
philosopher in Philadelphia, in 1794, Mr. Rittenhouse stood foremost
among the members of the Philosophical Society in publicly
welcoming the exiled philosopher to the country which he had
chosen as the asylum of his declining years; and in expressing his
high sense of his estimable character, and of the vast accessions
which he had brought to science. I often met Dr. Priestley at the
house of our friend. Their regard for each other was mutual. It is to
be regretted that their immediate intercourse with each other could
not be more frequent. Priestley had unfortunately chosen the
wilderness, instead of the capital or its vicinity, as his place of
residence: and Rittenhouse, alas! did not live two years after the
arrival of Priestley in America.

On the death of Mr. Rittenhouse, Dr. Priestley wrote me a letter of

condolence on the great loss which the publick had sustained; on the
irreparable loss which I, in particular, had suffered. When the Doctor
afterwards returned from Northumberland to Philadelphia, he
discovered much solicitude to know from me Mr. Rittenhouse’s
religious sentiments, and the manner and circumstances of his
death; and he evinced no small satisfaction in receiving from me that
relation which I have already given you, of the last hours, and of the
last words, of one of the best of men.

Mr. Rittenhouse had not studied natural history as a science: but

to some of the branches of this science he had paid particular
attention; and upon some of them he was capable of conversing with
the ablest, and the most experienced. In Botany, he was not
acquainted with the scientific or classical names: but the habits, and
in many instances, the properties of plants were known to him. I well
recollect how great were his pleasure and satisfaction, in
contemplating the Flora of the rich hills of Weeling, and other
branches of the Ohio, when I accompanied him into those parts of
our union, in the year 1785. In this wilderness, he first fostered my
love and zeal for natural history. Upon his return from the woods, in
the month of October, he brought with him, as ornaments to his
garden, many of the transmontain plants of the state of
Pennsylvania: and long before I knew that it grew wild in the vicinity
of Philadelphia, upon the banks of his native Schuylkill, he had
naturalized in his garden, the beautiful Silene virginica, which he
designated with the name of “Weeling Star.”

It is a fact, that in the last months of his life he devoted a good

deal of his time to an examination of the structure of the most
important organs of plants. Acquainted with that doctrine which
forms the basis of the sexual system, he was fond of examining
plants during the period of their inflorescence: and I remember, with
what apparent pleasure, he pointed out to me the tube in the styles
of some of the plants which grew in his garden.

He had made many observations upon the buds of trees, some of

which I think were new. I regret that the memorandums which he
kept of these observations have not been found among his papers.

Not fifteen days before his death, he had finished the perusal of a
German translation of Rousseau’s beautiful letters on Botany, which I
had put into his hands.

Mr. Rittenhouse, like Newton and many other men of great talents,
employed much of his time in the perusal of works on the subject of
natural and revealed religion. This was, I think, more especially the
case in the latter part of his life. Among other books which I could
mention, I well recollect that he read the Thoughts of the celebrated
French philosopher Pascall: and he acknowledged, that he read
them with pleasure. But that pleasure, he observed to me, was
diminished, when he learned, what was often the state of Pascall’s
mind:—a state of melancholy and gloom: and sometimes even of
mental derangement. At the time of his death, the American
Philosopher was engaged in the perusal of Mosheim’s Ecclesiastical
History: and he had just before finished the perusal of the
Meditations of the Emperor Marcus Antoninus; that excellent work,
replete with the sublimest morality, and with much of a sublime
religion.

About three weeks before his death, I had put into his hands the
first volume of Dr. Ferguson’s Elements of Moral and Political
Science. I took the liberty of particularly directing his attention to the
last chapter of the volume: the chapter on the future state. He read it
with so much satisfaction, that he afterwards sent it to his elder
daughter, with a request that she would peruse it.

The benevolent dispositions of our friend were well known to you.

You have, doubtless, done justice to this portion of his character; yet
permit me to mention a few detached facts, which have came under
my own immediate notice, and the relation of which may serve to
augment even your respect and veneration for Mr. Rittenhouse.

The year 1793 is memorable in the history of Philadelphia. During

the prevalence of the yellow fever, in the summer of that year, Mr.
Rittenhouse wrote to me a note requesting me to visit a number of
poor people, in his vicinity, labouring under the malignant fever; and
making it a condition of my attendance upon them, that I should
charge him for my services.

In the month of March of the same year, I had a good deal of

conversation with Mr. Rittenhouse, on the subject of penal laws. He
did not think that the late judge Bradford, whose essay on this
subject he greatly admired, and recommended to my perusal, was
too lenient in his views of the subject. He observed, that although he
had often served on juries, he thanked God, that he never had in any
case where life and death were immediately involved; observing, that
his conscience would ever reproach him, if he had, in any instance,
given his verdict for death. “Of all murders (he added) legal murders
are the most horrid.” He did not think that death ought to be the
punishment for any crime.

The union of sensibility with benevolence is frequently observed.

The sensibility of Rittenhouse was exquisitely nice; perhaps, I might
say, it was somewhat morbid. In a conversation which I had with him
on the subject of the analogies between animals and vegetables,
when I had observed to him, that the further we push our inquiries
into this interesting subject, the more reason we have for supposing,
that those two series of living beings constitute, as many eminent
naturalists have supposed, but one vast family, he said it appeared
so to him, but he hoped it would never be discovered that vegetables
are endowed with sensibility. “There is, he observed, already too
much of this in the world.”

His religion was sublime and pure. It had no tincture of superstition

or credulity. Accustomed, from an early period of his life, to
contemplate the largest and the smallest objects of Creation; and
with respect to the former to view their arrangement and harmony in
the construction of a system of immeasurable extent; in these
objects and in these places, he beheld one of the revelations of our
Creator. He could not be insensible of the ills, infirmities, and
miseries of human life, and even of the life of inferior animals. But
still he discovered, as he often observed to me, the existence and
even the dominion of much benevolence through the world. He was
wont to consider our benevolent dispositions, and our virtuous
affections, as among the strongest proofs of the existence of a
Creator. These dispositions, these affections, and our intellectual
powers, are the genuine emanations of a God.

Benjamin Smith Barton.

Philadelphia, December, 1813.

Letter from Lady Juliana Penn to the Rev. Peter Miller, Ephrata.

Septr. 29th. 1774.

Sir,

Your very respectable character would make me ashamed to

address you with words merely of form. I hope therefore you will not
suspect me of using any such, when I assure you I received the
favour of your letter with very great pleasure. And permit me, sir, to
join the thanks I owe to those worthy women, the holy sisters at
Ephrata, with those I now present to you, for the good opinion you,
and they, are pleased to have of me. I claim only that of respecting
merit, where I find it; and of wishing an increase in the world, of that
piety to the Almighty, and peace to our fellow-creatures, that I am
convinced is in your hearts: and, therefore, do me the justice to
believe, you have my wishes of prosperity here, and happiness
hereafter.

I did not receive the precious stone, you were so goad to send me,
till yesterday. I am most extremely obliged to you for it. It deserves to
be particularly distinguished on its own, as well as the giver’s
account. I shall keep it with a grateful remembrance of my
obligations to you.

Mr. Penn, as well as myself, were much obliged to you for

remarking to us, that the paper you wrote on, was the manufacture
of Ephrata: It had, on that account, great merit to us; and he has
desired our friend, Mr. Barton, to send him some specimens of the
occupation of some of your society. He bids me say, that he rejoices
to hear of your and their welfare.

It is I that should beg pardon for interrupting your quiet, and

profitable moments, by an intercourse so little beneficial as mine; but
trust your benevolence will indulge this satisfaction to one who
wishes to assure you, sir, that she is, with sincere regard, your
obliged and faithful well-wisher,

Juliana Penn.

Mr. Peter Miller, President of the Cloister at Ephrata.

To the Memory of the Honourable Thomas Penn, Esq. who died

March 21. 1775.

Peace, worthy shade! Peace to thy virtuous soul;

Life’s contest past, thou now hast gain’d the goal,
Destin’d for honest innate truth, like thine,
Where moral goodness rises to divine.
True to thy friendship, sacred to each trust,
In every duty most exactly just:
A princely wealth fill’d not thy heart with pride,
Thou nobly cast the glitt’ring bait aside;
Made it subservient to some useful aim,
 Some gen’rous purpose, or some proper claim:
As bounteous streams in pleasing currents glide,
It roll’d, refreshing, like some charming tide;
Cheer’d the lone widow in her humble dome,
And scatter’d comfort o’er her lonely home.
Thy guardian angel snatch’d thee from below,
E’er Pennsylvania was consign’d to woe:
Thou now may’st view, without one kindred tear,
What we deem harsh, oppressive and severe;—
Life’s motley picture, at one view, may’st scan,—
Unwind its tangled, complicated plan,—
Where this great truth is clearly understood,
That “partial evil’s universal good.”
In broken parts, man the dark system spies,
While all lies open to celestial eyes;
The links, united, of our scatter’d chain,
Shew why Penn suffer’d tedious years of pain,—
Shew why one patient virtuous mind doth mourn,
And why sweet Peace is from a people torn.
For, individuals of earth’s humble vale
Mount, in gradation, on a heav’nly scale:
Yet Virtue, only, has a charm in death;
Wealth droops his plumes, as man resigns his breath;
Its social merits can’t ascend the skies,
Terrestrial substance can’t to heav’n arise;
Too gross to enter the abodes divine,
In earthly darkness it can only shine.

Letter from General Washington to the Writer of these Memoirs.

Mount Vernon, Sep. 7th. 1788.

Sir,

At the same time I announce to you the receipt of your obliging

letter of the 28th of last month, which covered an ingenious essay on
Heraldry, I have to acknowledge my obligations for the sentiments
your partiality has been indulgent enough to form of me, and my
thanks for the terms in which your urbanity has been pleased to
express them.

Imperfectly acquainted with the subject, as I profess myself to be;

and persuaded of your skill, as I am; it is far from my design to
intimate an opinion, that Heraldry, Coat-Armour, &c, might not be
rendered conducive to public and private uses, with us,—or, that
they can have any tendency unfriendly to the purest spirit of
Republicanism: on the contrary, a different conclusion is deducible
from the practice of Congress and the States; all of which have
established some kind of Armorial Devices, to authenticate their
official instruments. But, sir, you must be sensible, that political
sentiments are very various among the people in the several states;
and that a formidable opposition to what appears to be the prevailing
sense of the Union, is but just declining into peaceable
acquiescence. While, therefore, the minds of a certain portion of the
community (possibly from turbulent or sinister views) are, or affect to
be, haunted with the very spectre of innovation;—while they are
indefatigably striving to make the credulity of the less-informed part
of the citizens subservient to their schemes, in believing that the
proposed General Government is pregnant with the seeds of
Discrimination, Oligarchy and Despotism;—while they are
clamourously endeavouring to propagate an idea, that those whom
they wish, invidiously, to designate by the name of the “well-born,”
are meditating in the first instance to distinguish themselves from
their compatriots, and to wrest the dearest privileges from the bulk of
the people; and while the apprehensions of some, who have
demonstrated themselves the sincere, but too jealous, friends of
Liberty, are feelingly alive to the effects of the actual Revolution and
too much inclined to coincide with the prejudices above described,—
it might not perhaps be advisable to stir any question that would tend
to reanimate the dying embers of faction, or blow the dormant spark
of jealousy into an inextinguishable flame. I need not say, that the
deplorable consequences would be the same, allowing there should
be no real foundation for jealousy: (in the judgment of sober reason,)
as if there were demonstrable, even palpable, causes for it.
 I make these observations with the greater freedom, because I
have once been a witness to what I conceived to have been a most
unreasonable prejudice, against an innocent institution: I mean, the
Society of the Cincinnati. I was conscious that my own proceedings
on that subject were immaculate. I was also convinced, that the
members,—actuated by motives of sensibility, charity and patriotism,
—were doing a laudable thing, in erecting that memorial of their
common services, sufferings and friendships;—and I had not the
most remote suspicion, that our conduct therein would have been
unprofitable, or unpleasing to our countrymen. Yet have we been
virulently traduced, as to our designs: and I have not even escaped
being represented as short-sighted, in not foreseeing the
consequences,—or wanting in patriotism, for not discouraging an
establishment, calculated to create distinctions in society and
subvert the principles of a republican government. Indeed, the
phantom seems now to be pretty well laid; except on certain
occasions,—when it is conjured up, by designing men, to work their
own purposes upon terrified immaginations:—You will recollect there
have not been wanting, in the late political discussions, those who
were hardy enough to assert, that the proposed General
Government was the wicked and traitorous fabrication of the
Cincinnati!

At this moment of general agitation and earnest solicitude, I should

not be surprised to hear a violent outcry raised, by those who are
hostile to the New Constitution, that the proposition contained in your
paper had verified their suspicions, and proved the design of
establishing unjustifiable discriminations. Did I believe that to be the
case, I should not hesitate to give it my hearty disapprobation. But I
proceed on other grounds:—Although I make not the clamour of
credulous, disappointed, or unreasonable men, the criterion of Truth;
yet, I think, their clamour might have an ungracious influence at the
present critical juncture: and, in my judgment, some respect should
not only be paid to prevalent opinions,—but even some sacrifices
might innocently be made to well meant prejudices, in a popular
government. Nor could we hope the evil impression would be
sufficiently removed, should your Account, and Illustrations, be found
adequate to produce conviction on candid and unprejudiced minds.

For myself, I can readily acquit you of having any design of

facilitating the setting up an “Order of Nobility:”—I do not doubt the
rectitude of your intentions. But, under the existing circumstances, I
would willingly decline the honour you have intended me, by your
polite Inscription; if there should be any danger of giving serious
pretext (however ill-founded in reality) for producing or confirming
jealousy and dissention, in a single instance; when harmony and
accommodation are most essentially requisite to our public
prosperity,—perhaps, to our national existence.

My remarks, you will please to observe, go only to the expediency,

not to the merits of the proposition: what may be necessary and
proper hereafter, I hold myself incompetent to decide; as I am but a
private citizen. You may, however, rest satisfied, that your
composition is calculated to give favourable impressions of the
science, candour and ingenuity, with which you have handled the
subject; and that, in all personal considerations, I remain with great
esteem, Sir, your most obedient and most humble servant,

Go. Washington.

Wm. Barton, Esq.

Dr. Benjamin Rush.

The foregoing Memoirs were entirely completed and prepared for

the press, before the decease of this Professor occurred; as is
mentioned in the preface.

Benjamin Rush was born in the county of Philadelphia, on the

twenty-fourth day of December, 1745, O.S. Having graduated in the
Arts at Princeton College, in the autumn of the year 1760, and
afterwards studied medicine under the direction of the late John
Redman, M. D. of Philadelphia, he completed his medical education
at the University of Edinburgh; where he received the degree of
Doctor in Medicine, in the spring of 1768. Returning to Philadelphia
in the summer of 1769, he was, on the 31st of July, in that year,
appointed Professor of Chemistry, in the College of Philadelphia; that
chair having been supplied for some time before, by the late John
Morgan, M. D. F. R. S. &c. About twenty years after this appointment
(viz. in 1789), he succeeded Dr. Morgan in the Professorship of the
Theory and Practice of Physic, in the same College: and in the year
1791, on the union of that College with the University of
Pennsylvania, he was chosen Professor of the Institutes and
Practice of Physick, &c. in the conjoint institution.

At divers times, and on various occasions, his talents were

employed in affairs of political concern. Besides having held, at
different periods, several other public stations, he was appointed a
member of Congress for Pennsylvania, on the 20th of July, 1776:
when he, together with some of his colleagues, appointed at the
same time, subscribed the Declaration of American Independence;
which great national act had received the sanction of congress, and
been generally signed by the members, sixteen days before.

He died of a typhus fever, in Philadelphia, on the 19th day of April,

1813; being then advanced a few months beyond the sixty-seventh
year of his age.

At the time of his decease, Dr. Rush was Professor of the

Institutes of Medicine, of the Theory and Practice of Physic, and of
Clinical Medicine, in the University of Pennsylvania: to which chair,
vacated by his death, Dr. Benjamin Smith Barton, Professor of
Materia Medica, Natural History and Botany, in the same institution,
was elected in the month of July, 1813.
 FINIS.

A1. The reader will find a very learned and interesting dissertation
on the astronomy of these and other nations of antiquity, in Lalande’s
Astronomie, liv. ii. W. B.

A2. Our orator might well pass on, without noticing more
particularly the fabulous annals of the Chaldeans. They assigned to
the reigns of their ten dynasties, 432 thousand years: and Lalande
observes, that this number, 432, augmented by two or by four
noughts, frequently occurs in antiquity. This prodigious number of
years expresses, according to the notions of the inhabitants of India,
the duration of the life of a symbolical cow: in the first age, this cow,
serving as a vehicle for innocence and virtue, advances with a firm
step upon the earth, supported by her four feet; in the second, or
silver age, she becomes somewhat enfeebled, and walks on only
three feet; during the brazen, or third age, she is reduced to the
necessity of walking on two; finally, during the iron age, she drags
herself along; and, after having lost, successively, all her legs, she
recovers them in the succeeding period, all of them being
reproduced in the same order.

The Bramins thus make up their fabulous chronological account of

the age of the world; viz.

The duration of the first age, 1,728,000 years

The second 1,296,000 do.
The third 864,000 do.
The fourth will continue 432,000 do.
Making the total duration of the world 4,320,000 years.

Mr. Lalande remarks, that these four ages have a relation to the
numbers 4, 3, 2, 1, which seem to announce some other thing than
an historical division. Therefore, to give this fabulous duration of the
world some semblance of truth. Mr. Bailly[A2a] rejects, in the first
place, the fourth age, of which, at present, (that is, when Lalande
wrote,) only 4887 years have passed: the residue of this duration
could not be considered by Bailly as any thing more than a reverie:
and as for the three first ages, he takes the years for days; in order
to shew, that, in reality, they reckoned by days, before they
computed by solar years. By these means, Bailly has reduced the
pretensions of the people of India to 12,000 years; and he identifies
this calculation for the Indians with that of the Persians, who give,
likewise, 12,000 years for the duration of the world. The accordance
thus produced in the two chronologies, seemed to Bailly to
strengthen the authenticity of the recital; and makes it appear, that
these notions prevailed alike among the Egyptians and the Chinese.

Such are the data, such the calculations, and such the reasoning
of Mr. Bailly, on this subject.

But, although Mr. Lalande has noticed the retrograde series of the
progressive numbers (1,) 2, 3, 4, in the Asiatic account of the age of
the world, a kind of mysterious constitution of the amount of the
years, in the several ages which make up the entire sum of its
duration, seems to have escaped the observation of that acute
philosopher; and probably the same circumstance passed also
unnoticed by Mr. Bailly: it may be considered as a species of
chronological abracadabra, engendered in the prolific brain of some
eastern philosopher: the following is the circumstance here meant. It
will be perceived, in the first place, that the arrangement of the
numerical figures, in making up the years allotted to the fourth age of
the world, is apparently artificial, and therefore, probably, altogether
arbitrary. It will then be seen, that the number of years in the third
age is double the amount of those in the fourth; that those in the
second is made up by adding together the years in the fourth and
third ages; and, that those in the first age are constituted by an
addition of the number of years in the fourth and second ages. This
being the fact, it does not seem to bear out Mr. Bailly, in his
hypothesis, and the calculations founded on it. W. B.
A2a. Mr. Bailly was the author of a History of Ancient and modern Astronomy.
His Essay on the Theory of Jupiter’s Satellites, which is said to be a valuable
treatise, was published in the year 1766. Both works are in the French language,
and were printed in France.

A3. Lalande observes that Mr. Bailly has gone back, in his
astronomical researches, to the first traditions of an antedeluvian
people, among whom there remained scarcely any traces of such
knowledge; and that he has presented us, in his work, with ingenious
conjectures and probabilities; or, more properly, appearances of
truth, (“vraisemblables,”) written with many charms of extensive
information. But, according to Mr. Lalande himself, all the ancient
astronomy down to the time of Chiron, which was about fourteen
centuries before the Christian era, may with probability be reduced to
the examining of the rising of some stars at different times of the
year, and the phases of the moon; since, long after that period, as
this great astronomer remarks, the Chaldeans and Egyptians yet
knew nothing of either the duration or the inequalities of the
planetary movements. W. B.

A4. See the preceding note.

A5. Some of the constellations appear to have been named, even

before the time of Moses, who was born 1571 years before Christ:
but, probably, most of them received their names about the time of
the Argonautic expedition, which took place in the year 1263, B. C

Hesiod and Homer who were co-temporaries, or, at least,

flourished nearly at the same time, that is to say, about nine
centuries before the Christian era, mention several of the
constellations; and, among the rest, the Bear and the Hyades: and it
is noticed by Mr. Lalande, that La Condamine says the Indians on
the river Amazons gave to the seven stars in the Hyades, the name
of the Bull’s-head, as we do; and that Father Lasitau tells us, the
Iroquois called that assemblage of stars to which we give the name
of the Bear, by the same name; and named the polar star “the star
that does not move.”

These are interesting facts. There is not the least resemblance,

whatever, in the two constellations which have been mentioned, to
the animals whose names they bear. Is it not, then, a matter of great
curiosity, as well as one which may prove important in its result, to
enquire, why two great tribes of uncivilized men, (supposed, by
some, to be aborigines,) in the northern and southern sections of the
western hemisphere, should apply the same denominations to two
assemblages of stars, by which those constellations were known to
Hesiod and Homer, if not earlier, and at least twenty-five hundred
years before? W. B.

A6. Hipparchus (of Nicæa, in Bithynia,) was a very celebrated

mathematician and astronomer of antiquity. Mr. Lalande styles him
the most laborious and most intelligent astronomer of antiquity, of
whom we have any record; and asserts, that the true astronomy
which has come down to us, originated with him. He divided the
heavens into forty-eight (some say forty-nine) constellations, and
assigned names to the stars. He is also said to have determined
latitude and longitude and to have computed the latter from the
Canaries; and he is supposed to be the first who, after Thales,
calculated eclipses with some degree of accuracy: but he makes no
mention of comets. Hipparchus died one hundred and twenty five
years before the Christian era. W. B.

A7. Friar Bacon is said to have been almost the only astronomer
of his age; he informs us that there were then but four persons in
Europe who had made any considerable proficiency in the
mathematics.

A8. Regiomontanus was born in the year 1436, at Kœnigsberg, a

town of Franconia, subject to the house of Saxe-Weimar. His real
name was John Müller: but he assumed the name of Regiomontanus
from that of the place of his nativity, which signifies Regius Mons.

This astronomer, who was greatly celebrated in his time, was the
first, according to Lalande, who calculated good Almanacks; which
he had composed for thirty successive years; viz. from 1476 to 1506.
In these (which were all published at Nuremberg in 1474, two years
before his death,) he announced the daily longitudes of the planets,
their latitudes, their aspects, and foretold all the eclipses of the sun
and moon; and these ephemerides were received with uncommon
interest by all nations. After noticing these, Lalande mentions the
ephemerides which are published annually at Bologna, Vienna,
Berlin, and Milan; but he pronounces the Nautical Almanack, of
London, to be the most perfect ephemeris that was ever published.
Regiomontanus compiled several other works, which greatly
promoted his reputation, He died in 1476, at the age of forty years.
W. B.

A9. See some interesting particulars respecting this great man in

Lord Buchan’s account of the Tomb of Copernicus, and in the note
thereto, inserted in the Appendix. W. B.

A10. Tycho-Brahé, as Lalande remarks, was the first who, by the

accuracy and the number of his observations, prepared the way for
the renewal of astronomy. The theories, the tables, and the
discoveries of Kepler, are founded on his observations; and Lalande
thinks, that their names, after those of Hipparchus and Copernicus,
ought to be transmitted with immortal honour to posterity.

Tycho was born in the year 1546, at Knudsturp in Scania in

Denmark, of a noble family, which subsisted also in Sweden under
the name of Brahé, and to which the marshal count Lœwendahl was
allied. He died in 1601, at the age of fifty-five years.

Frederick II, king of Denmark, gave to Tycho the little island of

Huen, called in Latin Venusin, towards the Sound, and about ten
leagues, northward, from Copenhagen: where that prince erected for
him a castle, named Uraniberg, and an observatory attached to it,
completely furnished with the best instruments. Yet only fifty-one
years after the death of Tycho, Mr. Huet, whose curiosity led him to
visit a place so celebrated could find no vestige of the observatory.
One solitary old man, who yet retained some recollection of it, told
him that the tempestuous winds to which they were subject along the
Sound, had demolished it. Even the name of Tycho was then
unknown in that savage island, as Mr. Lalande indignantly styles it:
and Mr. Picard, who was sent by the French academy, in 1671, to
ascertain the exact situation of the observatory, was obliged to have
the earth dug away, in order to discover its foundation. W. B.

A11. “Certain it is,” says the learned and pious Dr. Samuel Clarke
(in his Discourse on the Evidences of Nat. and Rev. Religion,) “and
this is a great deal to say, that the generality, even of the meanest
and most vulgar and ignorant people,” (among Christians,) “have
truer and worthier notions of God, more just and right apprehensions
concerning his attributes and perfections, deeper sense of the
difference of good and evil, a greater regard to moral obligations and
to the plain and more necessary duties of life, and a more firm and
universal expectation of a future state of rewards and punishments,
than, in any heathen country, any considerable number of men were
found to have had.”

In like manner, Archdeacon Paley (in his View of the Evidences of

Christianity) observes:—“Christianity, in every country in which it is
professed, has obtained a sensible, although not a complete
influence, upon the public judgment of morals. And this is very
important. For without the occasional correction which public opinion
receives, by referring to some fixed standard of morality, no man can
foretell into what extravagances it might wander.” “From the first
general notification of Christianity to the present day,” says the same
ingenious writer, “there have been in every age many millions,
whose names were never heard of, made better by it, not only in
their conduct, but in their dispositions; and happier, not so much in
their external circumstances, as in that which is inter præcordia, in
that which alone deserves the name of happiness, the tranquillity
and consolation of their thoughts. It has been since its
commencement, the author of happiness and virtue to millions and
millions of the human race.” He then asks: “Who is there, that would
not wish his son to be a Christian?” W. B.

A12. Some of the commentators inform us, that Mahomet taught

that the earth is supported by the tip of the horn of a prodigious ox,
who stands on a huge white stone; and that it is the little and almost
unavoidable motions of this ox which produce earthquakes.
 A13. Pythagoras, who was one of the most celebrated among the
Greek philosophers, in the knowledge and study of the heavens, was
born about 540 years before the Christian era. It is believed that he
was the first who made mention of the obliquity of the ecliptic, and of
the angle which this circle makes with the equator; although Pliny
attributes this discovery to Anaximander, whose birth was seventy
years earlier. Among the remarkable things which Pythagoras taught
his disciples, was the doctrine that fire, or heat, occupied the centre
of the world; it is supposed he meant to say, that the sun is placed in
the centre of the planetery system, and that the earth revolves
around him, like the other planets. He also maintained each star to
be a world; and that these worlds were distributed in an ethereal
space of infinite extent. W. B.

A14. Thales, who died about five centuries and an half before the
Christian era, in the ninety-sixth year of his age,[A14a] first taught the
Greeks the cause of eclipses, He knew the spherical form of the
earth; he distinguished the zones of the earth by the mean of the
tropicks and the polar circles; and he treated of an oblique circle or
zodiac, of a meridian which intersects all these circles in extending
north and south, and of the magnitude of the apparent diameter of
the sun.

Herodotus, Cicero, and Pliny, assert, as is noticed by Mr. Lalande,

that Thales had predicted, to the Ionians a total eclipse of the sun,
which took place during the war between the Lydians and the
Medes, But the manner in which Herodotus (who lived about one
century, only, after the time of Thales) speaks of this prediction, is so
vague, that one finds some difficulty in believing that it was fact, If it
were true, says Lalande, that Thales had actually foretold an eclipse
of the sun, it could be no otherwise, than by means of the general
period of eighteen years, of which he would have acquired a
knowledge from the Egyptians or the Chaldeans: for the period had
not yet arrived, when eclipses could be prognosticated by an exact
calculation of the motion of the moon. W. B.

A14a. But, according to Dufresnoy, he was born in the first year of the 35th
Olympiad, and died the first year of the 52d, those periods corresponding,
respectively, with the years 640 and 572, B. C.: and if so, he lived only sixty-eight
years.

A15. Alhazen was one of the greatest of the Arabian astronomers.

He went, about the year 1100, to Spain, where many of his nation
had established themselves in the eighth century, and carried thither
their knowledge of astronomy; yet, from the year 800 down to about
1300, science remained shrowded with the darkest ignorance,
throughout Europe.

Mr. Lalande observes, that the theory of Refractions is an

important one, in astronomy; although it was considered of little
consequence until the time of Alhazen. W. B.

A16. Aristotle, as though he had been of the race of the Ottomans,

thought he could not reign except he first killed all his brethren.
Insomuch as he never nameth or mentioneth an ancient author or
opinion, but to confute or reprove. Bacon. Advancement.

A17. Timocharis of Alexandria endeavoured, with Aristillus, a

philosopher of the same school, to determine the places of the
different stars in the heavens, and to trace the course of the planets.
Dr. Lempriere places him 294 years before Christ; and the Abbé
Barthelemy has inserted his name in the list of illustrious men, who
flourished in the fourth century before the Christian era: he probably
lived some time after the commencement of that century. W. B.

A18. By its peculiar situation it will continue to do so for a long

time.

A19. According to Lalande, Kepler was as celebrated in astronomy

by the consequences he drew from the observations of Tycho Brahé,
as the latter was for the immense mass of materials which he had
prepared for him: and the Abbé Delaporte (in his Voyageur François)
represents him as precursor of Descartes in opticks, of Newton in
physicks, and as a law-giver (“legislateur”) in astronomy.