by Nick Lane
Herrero, A., and Barja, G. ADP-regulation of mitochondrial free-radical production is different with complex I- or complex II-linked substrates: Implications for the exercise paradox and brain hypermetabolism. Journal of Bioenergetics and Biomembranes 29: 241–249; 1997.
Calorie restriction and free-radical leakage
Gredilla, R., Barja, G., and López-Torres, M. Effect of short-term caloric restriction on H2O2 production and oxidative DNA damage in rat liver mitochondria and location of the free radical source. Journal of Bioenergetics and Biomembranes 33: 279–287; 2001.
Sex versus survival
Kirkwood, T. B., and Rose, M. R. Evolution of senescence: Late survival sacrificed for reproduction. Philosophical Transactions of the Royal Society of London B: Biological Sciences 332: 15–24; 1991.
Aerobic capacity of birds
Maina, J. N. What it takes to fly: The structural and functional respiratory refinements in birds and bats. Journal of Experimental Biology 203: 3045–3064; 2000.
Index
Italic numbers denote references to illustrations. References to footnotes are followed by ‘n.’.
absorption spectra, respiratory pigments 74–5
ADP (adenosine diphosphate) 79; see also ATP (adenosine triphosphate)
aerobic capacity hypothesis (evolution of endothermy) 180–5
aerobic scope 168–70
African Eve 3, 242, 246, 251
ageing:
cell loss 303
exercise paradox 273, 306
free-radical leakage 272–3, 274–5, 277, 303–11
metabolic rate 158, 269–70, 272
mitochondrial mutations 284–8, 296–301
mitochondrial theory of 4, 272–301
theories of 272–3
see also lifespan
age-related (degenerative) diseases 4, 270, 271–2, 295–301, 303
algae, evolution of 25
Allen, John 138, 143–4, 144, 289–90
Altmann, Richard 12–13
Alzheimer’s disease 298
amino acids 10
amoeba, phagocytosis, and the cytoskeleton 35, 38–9, 44
Amoeba dubia 31, 121, 186
Anbar, Ariel 62
Andersson, Siv 44, 45, 49–50, 116, 117
antibiotics, effects on bacteria 38, 41
antioxidants and lifespan 274–7, 303–4
apoptosis (programmed cell death) 5, 191
balance with cell division 204
caspases 206–7
cells with faulty mitochondria 296
control by mitochondria 5, 202, 207–11
death genes 205–7
embryo development 203–4
failure as cause of cancer 5, 202 205–7
human body 215
immune function and 204
machinery used to signal fusion 221–5
origin of the term 204
origins of apoptotic proteins 212
role of cytochrome c 209–11, 260
sequence of events 204–5
threshold for 296, 299–300
triggers for 207–11
Archaea (prokaryotes) 28–9, 39–41
see also methanogens
archezoa (eukaryotes without mitochondria) 41–4, 46–7
asteroids, as source of organic material 95–6
ATP (adenosine triphosphate) 77, 79
‘high energy’ bond 80–1
mechanisms of ATP synthesis 81–4, 93
product of fermentation 79–80
product of photosynthesis 80
product of respiration 80
reservoir of potential energy 79–81
ATP pump, evolution in eukaryotes 61
ATPase (ATP synthase) 77, 82, 83
mechanism of ATP formation 90–1
proton-motive force 86–7, 87
reversal of synthesis process 91, 93
structure of 90–1
Attardi, Giuseppe 286–7, 293
Avery, Oswald 29
bacteria (prokaryotes) 8–9, 29–30
autotrophic 21–2
cell as the unit of selection 193–8
common inheritance with eukaryotic cells 35
competitive selection pressures 130
C-value (total DNA content) 31
death proteins 215–18
differences to eukaryotic cells 30–5
diversity without complexity 109
DNA 9, 10, 31–2, 115
energy sources 91
gene gain by lateral gene transfer 118–21
gene loss 116–19, 120–1
genome size 31, 115, 120–1
living inside other bacteria 59
locomotion using proton-motive force 92–3
loss of cell wall 38–9, 122–5
membrane transport systems 85–7, 87
multicellular colonies 25
proton-motive force 91–3
selfish gene concept 193–8
size and complexity limitations 121–3, 127, 128, 128, 144–7
size of 30
species definition 119–20
speed of cell division 114–15
structure 33, 34–5
sulphate-reducing 28–9
surface area-to-volume ratio 121–2
survival in extreme conditions 21–2
Barja, Gustavo 277, 304, 306–7
Barritt, Jason 263
bats, energy requirements for flight 308–9
Bdellovibrio 59, 213
Benda, Carl 13
Bennett, Albert 180–1
bioenergetics 6, 67–70
biophilic universe 22
birds:
degenerative diseases 271–2
energy requirements for flight 308–9
lifespan and metabolic rate 269, 270, 271
reduction of free-radical leakage 304, 305–7
Bishop, Charles 169
Black Sea, stratification 62–3
‘black smokers’ (hydrothermal vents) 99–100, 100 n.
Blackstone, Neil 219, 221–3, 224–5
body mass, and metabolic rate 156–61, 160, 270, 271; see also size increase
bone, strength-to-weight scaling 174–5
Bowler, James 253
Brand, Martin 183
Brody, Samuel 159, 167
Brown, James 160–6, 168
Buchner, Louis 78–9
Buss, Leo 198
Caenorhabditis elegans (nematode) 205–7
Calment, Jeanne 270 n.
calorie restriction, and lifespan 276–7, 306, 308
cancer 5, 200–2, 204, 215
Cann, Rebecca 242, 244–7
capillary density, and tissue demand 171–3
caspases 206–7, 212
catalysts 73, 95, 99–102
enzymes (biological catalysts) 78–9
Cavalier-Smith, Tom 36–7, 38, 41–2, 221
cell, as the unit of selection 193–8, 201
cell biology 8–11
cell death, necrosis 203, 205; see also apoptosis
cell membranes, evolution of 98–102, 101, 103–4, 133–5
cell organelles, as symbionts 13–14
cell wall, loss of 34–5, 38–40, 122–7
chemiosmosis 7, 68, 86
chemiosmotic hypothesis of respiration 86–91
chlorophyll, absorption spectrum 75
chloroplasts 13–14, 15, 33–4, 132
chromosomes 9–10
combinations of X and Y 229–31
number anomalies 262–3
telomeres and ageing 272
Clark, Graham 46–7
coenzyme Q 77
coenzymes 76, 77
colonies of cells 198, 215
complexity, evolution of 151–5, 185–7
convergent evolution 56
Conway Morris, Simon 23, 24, 217
Cope’s Rule 154
Cormack, James 203
Cosmides, Leda 237
Crick, Francis 9, 10, 68
; Cummins, Jim 253
Currie, Alastair 203
Cutler, Richard 276
C-value (total DNA content) 31
C-value paradox 31, 186
cyanobacteria 34
cytochrome c 74, 76, 77, 209–11, 260
cytochrome c gene 211–12
cytochrome oxidase 76, 77, 141–3, 290–1
cytochromes 74–5
cytology 8–11
cytoplasmic heredity 15
cytoskeleton, presence in some bacteria 38–9
Danielli, James 15
Darveau, Charles-Antoine 176
Darwin, Charles 151–2, 191, 238
Darwinian evolution 107–13
Darwinism, neo-Darwinism, ultra-Darwinism 192, 196–8
Dawkins, Richard 24, 35, 192–4, 196–8, 252
de Duve, Christian 27, 29
de Gray, Aubrey 279–80
degenerative diseases, see age-related (degenerative) diseases
Dennett, Daniel 111
diabetes, vulnerability to 255–6
DNA 9–11, 31, 68, 94; see also mitochondrial DNA
Dodds, Peter 167
Drosophila metabolic rate 270
Dunnet, George 269
ectothermy 178, 179
Else, Paul 181
Embley, Martin 52–3
embryo, selection of mitochondrial genes 262–5
Emory classification 254
endosymbiosis 13–14, 51, 109–13, 112
endothermy:
advantages of 178, 179
aerobic capacity hypothesis 180–5
birds and mammals 179, 180–1
dangers of free-radical formation 182–3
energetic costs 179–80
heat generation by proton leakage 183–4
and metabolic rate 180–5
energetic efficiency, and size 173–6, 185–7
energy, in molecular bonds 73
energy generation: bacteria 67
human body 67
redox reactions 72
the sun 67
see also ATP; proton-motive force
Engelhardt, Vladimir 79–80
Enquist, Brian 160–3
Entamoeba histolytica (cause of amoebic dysentery) 43, 46–7
enzymes (biological catalysts) 10–11, 78–9, 95
eukaryote evolution 25–6
drive for size and complexity 29–30, 125–7, 151–5
free radicals used to signal fusion 221–5
gene transfer 58–9, 59–61
predation 126–7
selection pressures 56–7, 61–3
eukaryote origins 19, 131–5, 145–7
bottleneck thesis 27–9
common inheritance with bacteria 35
fusion of host cells 219–21
gene sequencing used to identify 47–8
hydrogen hypothesis 36–7, 51–64, 54, 58–9
death apparatus 211–14, 215–19
loss of cell wall 34–5, 38, 125–7
mainstream view of origin 36–7, 38–50
mitochondria and 5–6
mitochondrial manipulation 219–21
‘Ox-Tox’ hypothesis 45–6, 49–50
possible form of first cell 49–50
possible initial bacterial association 44–6
possible methanogen ancestor 48–50, 51–64
possible origin by parasitic infection 44–6, 216–18
source of machinery of death 211–14
eukaryotic cells:
cell membranes 133–5
C-value (total DNA content) 31
differences to bacterial cells 8–10, 30–5
DNA arrangement 32
energetic cost of complexity 32
genes for archaeal lipids 135
genome size (total number of genes) 31
internal cytoskeleton 34–5
membrane structures inside 32–4, 33
nuclear membrane 32–3, 33
nucleus 30–1, 133–5
organelles 33, 33–4
size of 30
structure 9–11
Euler, Hans von 79
evolution:
biophilic nature of the universe 22
contingency versus convergency 23–4
gene-centred approach 192–8
macro-mutations 30
multicellular organisms 24–6
and purpose 107–8
religious view of 107, 151–2
exercise paradox (of ageing) 273, 306
Eyre-Walker, Adam 248–9
fermentation 78–9
evolution of 95–8
and phagocytosis 127
synthesis of ATP 79–80
flight, evolution of 23–4, 308–10
forensic use of mitochondria 3, 250–1
Fox, George 40
fractal model, geometry of supply networks 161–70, 171, 181 n.
Frade, José 213, 217, 218
free radicals 92, 172
formation of 140–2, 182–3
and mitochondrial mutations 278–80, 292–6
free-radical detection system 142, 310
free-radical leakage 4, 289
and ageing 272–3, 274–5, 277, 303–11
mitochondrial feedback signal 290–1, 302–3
and mitochondrial spare capacity 306–11
sexual fusion initiation 221–6
threshold for apoptosis 299–300
Galileo 175
Galton, Francis 252
gene, as unit of selection 192–8
gene number:
asexual limit 153
and sex 153, 186–7
gene sequencing:
archezoa 42–3
search for the prototype eukaryote 47–8
gene transfer:
bacterium to host 58–9, 59–61
from mitochondria to the nucleus 16, 47, 131–2
origin of the eukaryotes 58–9, 59–61
origin of the nucleus 134
genes 9, 10
accumulation and size increase 186–7
loss 116–17
mutation 10, 194, 200–1
see also mitochondrial genes
genome 10
duplication or union of 108–9, 110, 197
generation of random variation 108, 109
human genome project 68, 132–3
human mitochondrial genome 16, 281
increasing the number of genes 108–9
Giardia lamblia (intestinal parasite) 43, 47