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), 60-61Evolution’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.