The Equations of Life
Page 38
But what about the emergence: However, for a persuasive view that even multicellularity could emerge through the operation of simple physical principles (and may therefore be inevitable), see Newman SA, Forgacs G, Müller GB. (2006) Before programs: The physical origination of multicellular forms. International Journal of Developmental Biology 50, 289–299.
Although we cannot easily repeat evolution: We can, of course, find vestigial organs and genetic signposts that might reveal contingency and past history at work in fashioning an organism. We might also compare past evolutionary pathways up to an extinction event with those that occur afterward. For example, we might look at the evolution of the reptiles and compare them with the evolution of mammals after the end-Cretaceous. However, these are not controlled experiments in rerunning the sequence of evolution, since the environment has also changed, making it difficult, maybe impossible, to truly determine what is contingent and what is a consequence of altered conditions in which the organisms have been molded. We can more easily run evolutionary experiments in the laboratory and in certain well-controlled field settings to probe the role of contingency. For an excellent summary of research, from lizards to guppies and microbes, I recommend Losos J. (2017) Improbable Destinies: How Predictable Is Evolution? Allen Lane, London. However, experiments in the laboratory or even in the field still do not recapitulate the messy realities of Earth’s history.
We can deepen our ability: I am reluctant to go as far as suggesting a periodic table of life, a suggestion made in McGhee G. (2011) Convergent Evolution: Limited Forms Most Beautiful. Massachusetts Institute of Technology, Cambridge, MA, because although life forms may be limited, the term periodic table gives the impression that the scope of the evolutionary process has a parity with the simplicity of the atomic structure of elements and a periodicity in structure akin to that of electron stacking. Although I discuss the physical principles at the heart of evolution, I do not claim that the result of the canalization of life by physical principles is a set of life forms as simple as atomic structure. Perhaps a better term would be something like matrix of living forms. Nevertheless, the idea of classifying life systematically in a tabular format broadly similar to the periodic table and according to some agreed-on parameters is an exciting one. Such a classification would be one way to formalize the limits in living form. Similar attempts may be valuable in categorizing niches. See Winemiller KO, Fitzgerald DB, Bower LM, Pianka ER. (2015) Functional traits, convergent evolution, and the periodic tables of niches. Ecology Letters 18, 737–751.
For instance, the fusiform, sleek body: George McGhee states without ambiguity, “I predict with absolute confidence that if any large, fast-swimming organisms exist in the oceans of Europa—far away in orbit around Jupiter, swimming under the perpetual ice that covers their world—then they will have streamlined, fusiform bodies; that is, they will look very similar to a porpoise, an ichthyosaur, a swordfish, or a shark.” Although large sea creatures in the oceans of Europa are less likely than microbes—if there is any life at all—his point about the physical influence on convergent evolution at the level of the organism and its implications for a notion of universal biology is clear. See McGhee G. (2007) The Geometry of Evolution. Cambridge University Press, Cambridge, 148.
This understanding might greatly simplify: The observations of convergence at different levels of life’s structural hierarchy also offer hope for simplifying rules of assembly of living things. For example, for a comparison with convergence at the level of whole organisms, see Zakon HH. (2002) Convergent evolution on the molecular level. Brain, Behavior and Evolution 59, 250–261.
In the finale to his seminal book: Conway-Morris. S. (2004) Life’s Solution: Inevitable Humans in a Lonely Universe. Cambridge University Press, Cambridge.
Reductionism: I am not a militant reductionist; nor is this book another tired attempt to reduce biology to its simplest physical principles. I echo Mayr’s views that reductionism often destroys information at higher levels of a hierarchy, particularly in complex biological systems, since at higher levels, interactions between components often generate properties not manifest in their separate parts (see, for example, Mayr E. [2004] What Makes Biology Unique? Cambridge University Press, Cambridge, 67). Indeed, the investigation of self-organization and emergent complexity rests on the understanding that behavior at higher levels of biological hierarchy is not merely the sum of behaviors observed at lower hierarchies. As I have illustrated in Chapter 2 and elsewhere in this book, physical principles and equations can be applied to holistic biological entities such as flocks of birds or ant nests. A synthesis of physics and biology need not imply the age-old desire to break down biological phenomena into their tiniest parts, although historically this has often been the case and is often useful to do so.
INDEX
A. See adenine
accoutrements, 98
Acetobacterium woodii, 151
Achilles’ heel, of silicon, 190
acidophiles, 121
acrylonitrile, 179
actin (protein), 36–37
adaptations
of cell wall, 96
genetics used to encapsulate, 58
restrictions to, 10–11
to salt, 117
to temperature, 110, 114–115
adenine (A), 126–128, 132
adenosine diphosphate (ADP), 149, 160–161, 164
adenosine triphosphate (ATP), 36, 149–150, 156, 163
adhesion, equations for ladybug, 40–42
ADP. See adenosine diphosphate
aerobic respiration, 101–102, 146–147, 156–160
aerodynamics, 33, 37, 39, 44, 50, 251
airfoil, 44, 72, 236
alien life, 15, 157–158, 214–215, 221, 223, x
alkali flies (Ephydra hians), 121
alkaliphiles, 121
α-helices, 142–143
ammonia (NH3), 154–155, 172–174, 180, 183
anammox bacterium, 155
Antarctica, 65, 119–120
antibiotics, 98
ant-like creatures, 38
ants, 19–20, 23, 233, 249, 257
evolutionary pressures of, 30–31
messages between, 26
nests of, 21–22, 25, 38
oddities of behavior of, 27–29
populations of, 22, 24
self-organizing of, 35
APM 08279+5255, 181–182
appall, of creatures, 257
Arabian Desert, 72
archaea, 98
Armstrong, John, 230
Arrhenius, Svante, 175–176
Arrhenius equation, 175–176
arsenobetaine, 210
Artemia monica (brine shrimp), 121
Arthropleura (millipede), 53
Artisan Cheesecakes, Bruntsfield (fictitious shop), 26–27
astrobiology, 153, 157, 195–196, 226
astrophysical violence, 1
Atlas of Our Universe (Gallant), 15
atomic structure of life, 10, 215
ATP. See adenosine triphosphate
Australasia, x
autopod, 76
azotosome, 179–180
B = ρVg (buoyancy term), 74–76, 78–80, 232, 257
background radiation, 113–114, 176–177, 245
backyard, 86, 95
Baja California Sur, 116–117
Bali, ix–x
bar-magnets, 7, 168
barophiles, 123
Batman Returns (movie), 30
Benner, Steve, 174–175
β-sheets, 143
big bang, 182, 194
biochemistries, 16, 214
flexibility in, 135–136
laws of physics forcing, 100
metaphor for, 86–87
new turn in, 209–210
UV-screening compounds from, 80
water role in, 180–181
bioremediation, 155
bird flocking, 29–33, 38
birdbrain, 30
&nbs
p; birds, 249, 257
behavioral patterns of, 31–32
evolutionary pressures of, 30–31
heart-rate monitors on, 33
migration of, 34–37
reproduction of, 32
self-organization of, 29, 31, 35
bloodstream, 169
boatlike shapes, 191
borazine, 211
Boulby mine, 105–109, 116, 118–119
Boulby Underground Science Facility, 107
brine shrimp (Artemia monica), 121
Brock, Thomas, 110
Broda, Engelbert, 154–155
Bruntsfield, Edinburgh, 83
buoyancy term (B = ρVg), 74–76, 78–80, 257
Burgess Shale, 250–253
C. See cytosine
cafés, 145
caffeate, chemical, 151
cage-like, molecules as, 85, 87, 192
Canadian Rocky Mountains, 250
capillary action, 43
carbon, 2, 11, 189–194, 197–200
binding properties of, 213–214
as element of life, 111, 186, 203, 218, 229
carbon chemistry, 192–193, 196–205, 214–215, 218, 255
carbon dioxide gas, 13, 29, 61, 111, 147, 225
carbonaceous chondrites, 89
Carboniferous forests, 53
carbon-water bias, 215
Carroll, Sean, 72
Cassini spacecraft, 178
catch-up game, 178
C-C bond, 111
cell theory, 84–85
cell wall, 96, 98–99
cells
chemical reaction rules in, 16
collecting together of, 102
compartmentalization of, 90
development of skin, 78
Earth covered in, 99
electrical information transmitted by, 28
emergence of, 87–88
entities without, 86
as fundamental unit of life, 85, 99
as minuscule, 92–93, 99
molecule encoding information in, 7
naming of, 84
physical principles within, 104
pigments diffusing through, 36
predictability in development of, 95
as preexisting, 85
shape and rigidity of, 95–96
temperature influence on atoms in, 109–110
as veinlike, 103
water sucked from, 116–117
See also eukaryotic cells; multicellular aggregates; prokaryotic cells
cellularity, 86–87, 101, 218
See also multicellularity
CH3NO (formamide), 174–175
chaperonins, 110–111
Chaunax pictus (pink frogmouth), 77
chemiosmosis theorem, 150–151, 163–165
chemolithotrophs, 152
Chernobyl nuclear reactor, 162
chitin, 45, 46, 48, 56
CHNOPS elements, 205, 207–212
Chroococcidiopsis, 123
city dwellers, 26
clap and fling, 45
Cleveland Potash Limited, 106
cofactors, in proteins, 212
comet 67P, 203
compartmentalization, 85–86, 88, 90, 173, 237–238
complexity, emergence of, 149, 167, 200, 249, 254
computer gamers, 30
contingency, 44, 53, 83, 96–99, 144, 219, 250–257
convergent evolution, 42, 58, 60–64, 80, 219, 247
Conway-Morris, Simon, 256
Cooksonia (earliest land plants), 4
Copenhagen University, 201
Copernican revolution, 242
Cornell University, 179–180
Crick, Francis, 125–127, 135
CsB gene, 75
cyanobacteria, 156
cytochromes, 153
cytosine (C), 126–128, 130, 132
cytoskeleton, 36–37
Darwin, Charles, 17, 59, 81–82, 90, 231, 242
Darwinism, 5, 11, 69, 72, 144
Dawkins, Richard, 66
Deamer, David, 88–90
Death Valley, California, 121
degeneracy, 133
Deinacrida heteracantha (weta), 52–53
See also Godzillas
Deinococcus radiodurans, 123
dexterous, electrons as, 212
diffuse interstellar clouds, 168, 178, 196–199, 201
diffusion, 39, 55, 96
dilution, 85–86, 88
dinosaurs, 3, 52–53, 252
See also sauropsids
Disney, 30
divergence, 60, 75
DNA, 7, 71–72, 127–132
age before, 70
damages to, 245
discovery of, 125–126, 136
extracting of, 107
half-life of bonds of, 210
harboring strains of, 75
length of, 190
programming by, 36
radiation intersection with, 113
repairing of, 123
water binding to, 171
Don Juan Pond, 119–120
Doppler, Christian, 228
Doppler effect, 228
Dracula (movie), 105
dragonflies, 53
The Eagle Pub (Cambridge, England), 125
Earth, 4, 11, 140, 254–255
biological travelers on, 10
cells covering, 99
chemical reactions on, 89–90, 91–92
commonalities of all life on, 217
conditions for life production on, 204–205
crust of, 13
crystals and salts on, 213
endosymbiosis on, 102–103
energy from Sun received by, 146
environments of, 77–78
extremes on, 108
insect life on, 58
law of gravity as beginning of, 81–82
as nonexistent, 179
radiation from within, 113
simulating of, 203
Sun circled by, 14
temperature at center of, 109
temperature tolerance of, 111–113, 115–116, 121–123
view of life on, 158
See also super-Earths
earthworms, 63–64
ectotherm, 47
Ediacara Hills, Southern Australia, 252
Ediacaran period, 252–253
Edinburgh, 3–4, 145
Edinburgh Council, 27
Egyptian pyramids, 22
Eidgenössische Technische Hochschule, 130
electron acceptors, 147–148, 151–155, 229–230
electron transport chains, 153–154, 156, 158–166, 221
Enceladus (Saturn moon), 153, 181, 222
Endless Form Most Beautiful (Carroll), 72
endosymbiosis, 101–103
energy, 145, 198
for brain, 155–156
chemical change requiring, 246–247
Earth receiving, from Sun, 146
equation for producing, 146–147
of light, equation for, 78–79
minuscule amount of, 148
oxygen enabling access to, 160
potential sources of, 161–165, 180–181
predictability of best sources of, 230
Sun production of, 162–163
systems for gathering, 145–146, 149–150, 155, 220–221, 229–230
water gathering, 171–172
See also kinetic energy
Enterprise, starship, 185
entropy, 12
Eötvös Loránd University, 24
Ephydra hians (alkali flies), 121
Epulopiscium fishelsoni, 94, 96
error catastrophe, 220
Escherichia coli (flagella), 67–68
eukaryotic cells, 101–102
Europa (Jupiter moon), 181, 222
evaporation, rate of, 9
evo-devo (evolutionary developmental biology), 71–74, 81, 253–254
evolution, 59–60, 255, ix, x
as chessboard, 9
&n
bsp; contingency of, 99
environmental conditions driving, 88
equations channeling, in life, 58
as fickle, 108
forces shaping, 223
as inevitable, 104
limb development in, 76
oceans as analogy for, 8–9
process of, 5
radiation excess confronting, 123
rerun of, 99, 140–141, 233
selectivity of, 132, 135
specific routes of, 158
synthetic biology differing from, 141
transformation achieved in, 71
tricks of, 115
wheel-like contraptions experimented with in, 65–66
See also convergent evolution
evolutionary developmental biology (evo-devo), 71–74, 81, 253–254
exoplanets, 223–233, 237–238
extinctions, 231
extremophiles, 107–108
eyes, of insects, 55
faunas, 253, ix
feedback systems, 27–28, 56
See also negative feedback effect; positive feedback effect
fermentation, 161
Fick, Adolf, 51
Fick’s first law, 52
filmmakers, 30
fish, 7, 169, 249
equation for land transition of, 74–75
hydrodynamics dictating shape of, 69–70
oxygen use of, 51
swimming to walking transition of, 77
See also surgeonfish
Fish and Wildlife Service, US, 34–35
flagella (Escherichia coli), 67–68
flexibility, 3, 131
in biochemistries, 135–136
in development, 73–74
of elements, 213
of ladybug wings, 44
in life, 140
resilin for, 45
in tool kit, 139
walking requiring, 77
of water, 170
flight, power of, 3, 236–237
footholds, legs navigating, 65
formamide (CH3NO), 174–175
formose reaction, 201
4πr2, 93
Franklin, Rosalind, 125
Freeland, Stephen, 137–141
freezing-point-depression constant, 49–51, 113
freshwater, 167
friction, 55
frond-like creatures, 252
frozen accidents, 126, 129, 135, 140
Gallant, Roy, 15–16
gelateria, 200
genetic code, 12, 244, 250, 254–256
assembling of, 130
changes in, 72
developing of, 90–91, 125–126
differences produced in, 248
errors in reading, 133–134
as expanded, 141
forms of, 88
of ladybugs, 56
modifying, 129
as not accidental, 136
predictability and, 136