Index: Evolution's Clinical Guidebook

In the past few blogs, I've been discussing the recent publication of my book, Evolution’s Clinical Guidebook: Translating Ancient Genes Into Precision Medicine. The premise of this book is that modern medicine is based on an understanding of evolutionary processes. Evolution shows us the relationships between the subdisciplines of medicine that benefit directly from Precision Medicine (i.e., pathology, microbiology, clinical genetics, pharmacology, and bioinformatics). In Evolution's Clinical Guidebook, all of these diverse fields are brought together, under the subject of evolution. To illustrate, I have listed below the first few pages of the index to the book (letters A through H). Just by perusing these index terms, you can get some idea of the role played by evolution as the great unifier of modern medicine.

Partial Book Index

A 
Abiogenesis 
  catalysts, 2 
  cellular life, 
  earliest signs of, 4 
  definition, 1
  DNA, 4 
  evolution, 2 
  life on earth, 1 
  natural selection, 2
  RNA, 4­5
Acanthodians, 215
Acarnus erithacus, 192, 192f 
Acidianus Tailed Virus, 160
Acquired disease, 20, 29-­30
Actin, 17
Actinistia, 216
Actinopterygii, 215
Adaptive immune system, 214
Adaptive immunity, 161, 164
Adenocarcinoma, 125, 126-­127f Adult organisms, 94, 102
Agenesis of the Corpus Callosum (ACC), 222
Aging, 77, 216, 257-­258, 261-­265 
  vs. diseases of old people, 257-­259 
  evolution of, 252­-265 gene, 257­-258
Agnatha, 214
Allele, 77
Allium cepa, 66
Allium ursinum, 66 alphaA-Crystallin, 18
Alstrom syndrome, 213-­214
Alternative RNA splicing, 126
Amanita phalloides, 155
Amborella trichopoda, 150
Ambulacraria, 197
Amniotes, 218
Amoebozoa, 184, 290
Amphibia, 216­218
Amphioxus, 150
Amyloid world, 30
Anatomy, 246
Ancestral classes, 175-­176, 196­-197
Ancestral lineage, 12
Ancestral species, 12
  eukaryotic development, steps in, 14-­15, 15f 
  gene families, 13­-14
Ancylostoma duodenale, 292
Androgenesis, 221
Aneuploidy, 69­70, 70f Angelman syndrome, 222
Angiogenesis, 126
Angiosperma, 29­-44
Animal cells, 262
Animalia, 27f 
Animal model, human disease 
  Koch's postulates and reliance, 299-­300 
  nonhuman eutherians, 285 
  non-vertebrate models, cancer research, 298-­299 
  for orthodiseases
    Caenorhabditis elegans (nematodes), 294, 296-­298, 297f
    Danio rerio (zebrafish), 294, 297-­298, 298f 
    Drosophila melanogaster (fruit fly), 294, 297 
  homologous genes, 296 
  human pathologic processes, 295 
  orthologous genes, 295­-296
  Saccharomyces cerevisiae (yeast), 294­-296, 296f 
  rabbits, myxoma virus on, 300-­302 
  rats, 285 
  specificities and idiosyncrasies
    clinical trial, 286­-287
    Gram-negative organisms, 286 
    infections, history of, 290­-291, 293-­294 
    inflammatory response, 287 
    lipopolysaccharide, 286 
    mice, 286­288 
    microorganisms, potential pathogens, 288-­290 
    rodent models, 287-­288
  TGN1412, 286­287
Anlagen, 127
Aplastic anemia, 270
Apoikozoa, 186­-187
Apomorphy, 198
Apoptosis, 53
Archaea, 26, 27f 
Archaeplastida, 14-­15, 28, 186
Archiplastidae, 185
Arrhythmogenic cardiomyopathies, 191
Arthropods, hepatopancreas of, 118-­119
Ascaris lumbricoides, 292
Aspergillus flavus, 155
Association vs. cause, 77
Ataxia telangiectasia, 30
Atlantogenata, 229
Autism, 58
Autoantibody disease vs. autoimmune disease, 233
Autosomal dominance, 270
Azacytidine, 122

B 
Bacillus globigii, 288
Bacillus subtilis, 244
Bacteria, 26
Baraitser-Winter syndrome, 57
Bartonella species, 26
Basal cell carcinomas, 223-­224, 223f Basal layer, 255
Benign tumor, 218, 233
Bikonta, 183­184
Bilateria, 94, 193­203, 254
Bioinformatics, 78
Biological diversity, 152
Biological theory, 308
Biopsy specimen, 255f Biosphere, 157
Biosynthetic cycle, 17
BK polyomavirus, 292
Blastocystis hominis, 289
Blastula, 191
Blastulation, 189, 190f Blended class, 322, 325
Blood, photomicrograph of, 108f Bloom syndrome, 262
Bone marrow, 256
Bookie, 266
Bootstrapping paradoxes, 5
  chicken and egg paradox, 6­8 
  enzyme and enzyme-synthesizing machinery, 8 
  general solution for, 11-­12 
  hardware or software, 5­6 
  process of evolution and product of evolution, 9-­10
  RNA and DNA, 8­9, 10f 
  species and class of animals, 10-­11
Borderland of Embryology and Pathology, 118-­120
Boreoeutheria, 229
Borhing-Opitz syndrome, 57
Brassica oleracea, 158
BRCA, 271
BRCA1 gene, 269
BRCA2 gene, 269
Breast cancer, 260
Breeds, 248, 249f Brugia malayi, 292
Bryophyte life cycle, 7
Bryophytes, 7
BUB1B gene, 70
Bubonic plague, 292
Bungarus caeruleus, 110f "But-for" test, 30

C 
Caenorhabditis elegans, 65, 123, 294, 296-­298, 297f Calvin cycle, 17
Cambrian explosion, 21­-25, 21­-22f, 155-­156, 185 
  coexistence and coevolution, 25­26
  animals (class Metazoa), 28
  Archaea, 26, 27f 
  Archaeplastida (plants), 28 
  bacteria, 26 
  fungi, 28 
  single-celled eukaryotes, 28 
  viruses, 26
Cambrian period, 21-­22, 22f, 24
Cancer, 259­261
Cancer cells, 51
Cancer progression, 30
Carcinogen, 127
Carcinogenesis, 17, 30-­31, 223
Carcinoid tumors, 211
Carcinosarcomas, of uterus, 119
Caretaker diploid organism, 7
Carotenoids, 156
Carrier, 26, 31 asymptomatic, 27
Catarrhini, 231
Cause, 19, 24, 28
Cell types, epigenome and evolution of, 103-­115
Cell-type-specific gene expression, 112
Cenancestor, 37
Cephalochordata, 198­-203
Cercopithecoidea, 231
Chagas disease, 28, 269-­270
Chance occurrence, 9­10, 31
Channelopathy, 127
Charcot-Marie-Tooth disease, 261
CHARGE syndrome, 57
Chemical diversity, 154
Chemokine, 293, 301
Child class, 198
Chimeric Antigen Receptor for T cells (CAR-T) therapy, 157, 164
Chitin, 185
Chlamydia trachomatis, 292
Chloroplast evolution, 14­15, 17, 31
Choanoflagellatea, 186­187
Choanozoa. See Apoikozoa Chondrichthyes, 215
Chordata, 197­203
Chordoma, 198
Choriocarcinoma, 221
Chromatin, 156
Chromosomal disorder, 271
Chromosomes, 61
  number, variations in, 66
Chronic obstructive pulmonary disease (COPD), 271
Chytrids, 186
Cichlids, 153­154, 154f Ciliopathies, 213-­214, 233
Cis-acting vs. trans-acting, 127-­128
CISD2 gene, 264
Cisd2-null mice, 264
Clade, 128
Cladistics, 198
Class, 7, 32
  of animals, 10, 12, 24­-25 
  of cells, 6 
  of metazoan organisms, 25 
  of organisms, 4­5 
  of paradoxes, 5
Classification, 11 
  data retrieval, 176 vs. diagnosis, 199 
  flying animals, 175 
  formal definition of, 175 
  inferencing, 176 
  mammals, Aristotle, 173-­174 vs. ontology, 177, 198 
  pseudo-scientific assertion, 177 
  self-correction, 177 
  simplification, 175 swimming animals, 175 walking animals, 175
Classification system vs. identification system, 325
Class noise, 322. See also Blended class Clinical trial, 286-­287, 301
Clostridium feseri (blue bacteria), 107f 
Clustered Regularly Interspaced Short
  Palindromic Repeats (CRISPR), 251
Cnidaria, 193
Cnidarian organisms, 193, 195f Coccidia, 28
Cockayne syndrome, 262
Codon, 8, 32
Cofactor, 156, 165
Collision tumor theory, 120
Colon cancers, 119
Combined deficiency, 128
Commensal, 32­33
Competence of classification, 176
Complex disease, 33
Composition theory, 120
Congenital anomaly, 271
Congenital chondrodystrophy, 17-­18
Congenital disorder, 17-­18, 33
Congenital hemangiomas, 119
Connective tissue, 128
Contig disease, 271
Contiguous gene deletion syndrome, 271
Convergence, 165
Conversion theory, 120
Copy number, 78
Corbels, 239-­240
Cornelia de Lange syndrome, 112
Corpus callosum, 222
Cousin class, 167
CpG island, 128
CpG sites, 103
Cranial neural crest, 208
Craniata, 128, 148-­149, 198­-203, 207-­212
Craniates. See Craniata Crocodilia, 218
Crohn's disease, 273
Ctenophora, 193
Ctenophorans, 193, 194f Cyanobacteria, 14­15, 15f, 17, 23, 33
Cyclic neutropenia, 55
Cyclostomata, 211-­212
Cynodonts, 219
Cystic fibrosis transmembrane conductance regulator (CFTR), 113
Cytokine storm, 286-­287
Cytopenia, 78
Cytotrophoblasts, 229


D 
Danio rerio (zebrafish), 294, 297­-298, 298f Daphnia pulex, 154
Darwin's theory, 153
Decitabine, 122 delta1-Crystallin, 18
Demodex, 291
Demospongiae, 192
De novo disease mutations, 56-­58
De novo genes, 74­-76
De novo mutation, 78
Dense core granules, 210
Dermal bones, 209
Dermis, 255
Dermoptera, 230
Desmosomes, 187, 188f, 189, 190f, 191
Deuterostomia, 197
Deuterotomia, 148-­149
Developmental disorder, 128
Devolution, 241
Diagnosis vs. classification, 199
Diamond Blackfan anemia, 210
Diethystilbestrol (DES), 117
Differentiation, 78
Digenic disease, 128­-129
DiGeorge syndrome, 82
Dinosauria, 218
Diploid organism, 7
Dipnomorpha, 216
Dipnotetrapodomorpha, 216
Dipoblasts, 193
Direct mutagen, 52
Direct transdifferentiation, 111
DNA, 73­87
DNA-DNA reassociation kinetics, 151-­152
DNA methylation, 4, 33
DNA repair, 17, 33
Dollo's law, 271
Dormancy, 33
Down syndrome, 56
Driver pathway, 19, 34
Drosophila melanogaster, 101, 294, 297
Drug development, economics of, 20
Druggable driver, 34
Dysgerminomas in women, 102
Dyskeratosis congenita, 262
Dysplasia, 199


E 
Echidnas, 226
Echinodermata, 197
Ectoderm, 129
Eikenella corrodens, 289
Embryo, 99­103 vs. fetus, 129
Embryogenesis, 161
Embryology, relationship between evolution and, 93-­103
Embryonic anlagen, 102
Embryonic stem cell, 129
Endoderm, 6, 34
End-stage condition, 272
Enhancer, 78
Enigmatic pacific hagfish, 211-­212, 212f 
Enterocoelomata. See Deuterostomia Epidermis, 255, 256f 
Epigenome, 4, 34, 221
Epigenome disruptors, 121-­122
Epigenomic methylation, variations in, 65
Epimutation, 129-­130
Epipubic bones, 239
Epistasis, 34­35
Epithelial cell, 130
Epitheliozoa, 193
Epithelium, 189, 189f Erasure, 105-­106, 221
ERCC6 gene, 262
ERCC8 gene, 262
Etiology, 79
Euarchonta, 230
Euarchontoglires, 229-­230
Eugenics, 247-­252
Eugnathostomata, 215
Eukaryota, 15, 148­149
  Bikonta, 183-­184 eukaryotes, 179
  Excavata, 183-­184 
  mitochondria, 180 
  nucleus, 179, 182
  Podiata, 183­184 
  prokaryotic life forms, 179 
  single-celled eukaryotes, 179, 180f 
  Syringammina fragilissima, 179 
  undulipodia, 182
  Unikonta, 183-­184
Eukaryotes, 7, 67, 153­-155, 161, 176, 189
Eumetazoa, 191-­193
Euteleostomi, 215
Eutheria, 97-­98, 226-­235
Eutherians, 226-­235
Evo-devo, 130
Evolutionary convergence, 166
Evolutionary frustration, principle of, 248
Evolution, 
  as fantasy bacterial pathogen, 317­-319 
  disease diagnosis by symptoms, 321­-323 
  drug development and testing, 319 
  homologous genes, 316­317 
  science fiction aficionados, 324 
  speciation, 324 
  taxonomic organisms, treatments for, 319-­321 
  theory of intelligent design, 324-­326
Evolution deniers, 307
Evolvability, 153, 165
Exaptation, 35
Excavata, 183­184, 290
Exome sequencing, 79
Extraembryonic cells, 233
Extraembryonic tissues, 221, 233


F 
Facultative intracellular organism, 79
Fanconi anemia bone marrow failure, 257, 263
Female Anopheles mosquito, 107
Fetal period, 101
Filarial nematodes, 292
Filozoa, 186
First Law of Bioinformatics, 59
Fish, 118-­119
Forme fruste, 130
Founder effect, 13, 35
FOXL2 gene, 112
Fungi, 28, 186, 189


G 
Gallertoids, 130, 187, 191­192
Gametes, 6, 35, 148­-149
Gametic organism, 7
Gametophytes, 7
Gastrointestinal stromal tumors (GISTs), 19
Gastropods, 118-­119
Gene(s), 269
Gene conservation, 58-­61
Gene diversity, 154
Gene editing techniques, 251
Gene pool, 13, 26, 35, 58­61, 151­152, 314, 317­319, 324
Generalization, 35
Gene regulation, 35
Gene sharing, 18
Gene size, 66­67
Gene-targeted therapy, 19
Genetically engineered mouse (GEM), 233-­234
Genetic fine-tuning, 124­-138
Genetic heterogeneity, 130
Genetic instability, 79
Genetic mutations, 151
Genetic surplus disorder, 79
Genome, 12, 14-­15, 26, 35
Genome Wide Association Study (GWAS), 272
Genomic architecture, 64­73
Genomic disorder, 79
Genomic regulation, 76­87
Genomic regulatory processes, 125­138
Genomic regulatory systems, 
  pathologic conditions of, 121-­138
Genomic structural abnormalities (GSVs), 69
Genomic structural variation, 79
Germ cell, 6, 35
Germ cell line, 35­-36
Germ layers, 131
Germline, 79
Germline mutation, 80
Gestational trophoblastic disease, 234
Giant viruses, 162
Glires, 230
Globins, 13
Gnathostomata, 161, 214-­215
Gorillini, 232


H 
HACEK, 272
Haeckel's theory, 96-­97
Haemophilus influenzae, 244
Hair follicles, 223­224, 224f Hamartoma, 158, 166
Haploid, 7­8, 36
Haploid organisms, 7, 36
Haplorrhini/haplorhini, 231
Haplotype, 80
HAS2 gene, 248
Hemichordata, 197
Hepatitis B, 292
Hepatocyte, 100
Hepatoid adenomas, 119
Hepatoma, 131
Hereditary nonpolyposis colorectal cancer syndrome, 131
Heritability, 131
Heterokonts, 289, 301
Hirschspring disease, 209
Histone, 65, 199
Histone disruptors, mild effects of, 122
Histopathology, 131
Histozoa, 193
Hodgkin lymphoma, 273
Holometabolism, 156, 166
Holomycota, 186
Holozoa, 186
Holt-Oram syndrome, 123
Homeobox, 36
Hominidae, 231­232
Homininae, 232
Hominini, 232
Hominoidea, 231
Homo, 232
Homo erectus, 232
Homolog, 12, 18, 24, 36
Homologous genes, 316-­317
Homologous recombination, 
  during meiosis, 62
Homoplasy, 166
Homo sapiens, 147­149, 176, 232­235
Homozygosity, 80
Hookworms, 292
Horizontal gene transfer, 80
Horse, 
  gestation period of, 241f 
Horseshoe crabs, 149, 149f 
Host, 155­157, 159­161, 163, 166
HOX gene diseases, mild clinical course of, 123
HOX genes, 24
Human(s), 232­235
Human diseases, 115­118
Human embryo, dorsum of, 97f Human embryology, 246
Human embryonic stem cells, 100f Human gene pool, 55-­56
Human kidney, 101
Human phylogenetic lineage, 177­-179
Hutchinson-Gilford progeria syndrome, 263
Hydatidiform mole, 221, 234
Hydractinia carnea, 253
Hydrops-ectopic calcification-"moth-eaten" (HEM), 17-­18
Hylobatidae, 231
Hyperplasia, 273
Hypoxanthine-guanine phosphporibosyl transferase (HGPRT), 60­-61

Evolution’s Clinical Guidebook: Translating Ancient Genes Into Precision Medicine is available from Amazon or from the publisher's website. If you are fortunate enough to have full institutional access to ScienceDirect, you can download chapters at no cost.

Jules Berman

key words: evolution, precision medicine, genetics, rare disease, clinical genetics, bioinformatics, evo-devo, Jules J. Berman, Ph.D., M.D.