Key ideas from the work of A. Wagner on networks and diverse neighbourhoods

3. “Natural selection is not a creative
force. It does not innovate, but merely
selects what is already there”

4. “The real mystery of evolution is
not selection, but the creation of
new phenotypes”

5. https://en.wikipedia.org/wiki/Speciation
By Ilmari Karonen CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=961776

6. By Miguel Chavez - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=65759614
Punctuated equilibrium consists of
morphological stability followed by rare
bursts of evolutionary change via rapid
cladogenesis.
Phyletic gradualism, the more gradual,
continuous model of evolution. We see
equilibrium states separated by a jump
phase.

7. “Life is based on prosaic chemistry… Even
the largest changes in an organism result
from alterations in individual molecules”

9. http://www.zo.utexas.edu/faculty/sjasper/images/17.3.gifhttp://www.molecularecologist.com/wp-content/uploads/2016/01/central-dogma-enhanced.png

10. “The relationship between genotype and
phenotype is complex beyond imagination”

11. “Life appeared almost as soon as it could
appear. Life’s origins and the innovations behind
it might not be that hard to come by. I would not
be surprised if life arose many times”

12. “Metabolic innovation is combinatorial. Nature
experiments through gene shuffling at a staggering
scale. Everywhere on this planet, a relentless shuffling
and mixing and recombining of genes takes place”

14. “Even after 3.8 billion years of evolution, life has
explored only a tiny fraction of the library. The
metabolic library is packed to its rafters with
books that tell the same story in different ways”

15. “A genotype network: a connected network
of paths linking texts with the same
meaning that extends through the library”

16. “Different neighbourhoods contain different
novel phenotypes. Most metabolic
innovations are unique to one neighbourhood
and do not occur in the other”

17. “Genotype networks guarantee that evolving
populations can explore the library. But without
diverse neighbourhoods, exploring genotype network
would be pointless: the exploration would not turn up
many texts with new meanings”

20. “Minimal changes can have dramatic consequences
for life. Minute alterations of no more than a few
atoms can have effects that percolate through an
organism that is a million times as large and alter the
life of its descendants forever”

21. “Problems like catalyzing a chemical
reaction don’t have just one solution. Or
even a million solutions. They have
astronomically many solutions”

22. “An altered protein does not always lose its
function and meaning. Some alterations
impair neither folding nor function, and get
passed on to the next generation”

23. “Robustness: the persistence of life’s
features in the face of change”

24. “Even when the genotype has changed, there
need not be any change in the phenotype, in the
organism itself and its observable features. An
organism like this is robust”

25. “Nature must keep what works alive
while exploring the new”

26. “Neutral change is critical for navigating
genotype networks: a safe path to innovations
through treacherous territory. Once-neutral
changes can turn into essential parts”

27. “The astonishing fact that evolution needs to explore
one 10-100th of a library to secure the arrival of the
fittest goes a long way to explain how blind search
produces life’s immense diversity”

28. “Environmental change requires complexity, which begets
robustness, which begets genotype networks, which enable
innovations, the very kind that allow life to cope with
change, increase its complexity, and so on, in an ascending
spiral of ever-increasing innovability”

29. “Creativity comes from a single source: the
ability to explore vast and complex landscapes”

31. “An idea that is central to any science of creation:
the difficulty of a problem can be encapsulated in
the topography of its landscape”

32. http://4.bp.blogspot.com/-SiplaXn_BvI/UoObx8Z_xOI/AAAAAAAABxU/6a12tGh-1QU/s1600/fitness_landscape_smooth_rugged_2.png
Smooth and rugged fitness landscapes

33. “Single-peaked smooth landscapes correspond to
easy problems. Multipeaked landscapes
correspond to harder problems. The hardest
problems need the most creative solutions”

37. “Each cell type transcribes and translates into
protein only some of the 20,000 genes of our
genome. Some genes are only turned on in the
liver, others only in the brain, and so on”

38. “Where, when, and how often genes are transcribed and
translated is regulated by specialised proteins known as
transcriptional regulators. The basic principle: to make their
influence felt, regulators need to be close to where the
biochemical machinery starts transcribing: at the gene’s beginning”

39. “Each regulator can recognise and latch onto short DNA
words with specific sequences of letters (CATGTGTA or
AGCCGGCT); if such word occurs near a gene, the gene’s
transcription gets turned up or down”

40. “Gene regulation helps sculpt all multicellular organisms. A new
kind of body or even just a new body part requires new
regulation. All the product of life’s creativity require altered
regulatory recipes that guide genes to make a bit more or less of
their proteins a bit earlier or later. Subtle alterations that
manipulate the ingredients to create new life”

41. Genetic drifting: the change in the frequency of an existing
gene variant (allele) in a population due to random
sampling of organisms

44. “Drift causes random and directionless changes
in a population’s gene pool. Think of it as an
unceasing tremor that causes this landscape to
tremble. These tremors can take the population
in any direction –uphill, downhill, or sideways”

45. “Islands are graveyards of extinct species, but
also wellsprings of evolution’s creativity”

46. “In the smaller populations of larger organisms,
the influence of genetic drift is greater, and that
of selection is weaker than in larger populations
of smaller organisms”

47. “Many bad alleles that would be wiped out
quickly in a bacterial population are invisible to
natural selection and can persist in large animals
or plants”

49. “A typical vertebrate genome has 3 billion letters, almost 1000x as
many as that of E.coli [but] we don’t have that many more genes –less
than 7x more. Our greater number of genes cannot explain why our
genomes are so much larger. Most of the difference in genome size
comes from DNA outside of genes. Also called non-coding because it
does not encode any proteins”

50. “Our genome is a vast sea of non-coding DNA in which
our genes are but small islands that occupy a mere 3%
of the genome. [And] only a tiny fraction of human
non-coding DNA regulates genes”

51. “We do not know yet what –if anything- most of our
DNA is doing, but it is a giant playground for
evolution’s creativity”

52. “A genome can increase in size [by] DNA duplication, a kind of
mutation. The DNA text copied may comprise a few letters or
large parts of a chromosome with millions of letters. It may
comprise one or more genes”

53. “Mobile DNA aggressively promotes its own duplication. It
encodes one or more proteins with the ability to copy and
paste their coding DNA to some, usually arbitrary, location”

54. “When mobile DNA gets pasted near a gene, it can
inadvertently turn that gene on. When this happens, embryo
development can be altered dramatically or subtly”

55. “Subtle changes are more frequent than dramatic
ones, and so the damage is often slight, reducing the
host’s fitness by less than 1%”

56. “In large organisms, mobile DNA can steadily accrue
because populations are too small, drift is strong, and
selection is too weak to weed out mobile DNA with
subtle effects. The end result: more than 50% of our
genome has mobile origins”

57. “The result of all this genomic complexity is a giant playground for
evolution’s creativity. The more pieces a gene has, the more kinds of
proteins can be created by mixing and matching these pieces in new
ways. Our genes come in so many pieces that our body can make
50,000 more proteins than a fruit fly can, even though we have fewer
than twice as many genes”

58. “Random mutations stand a far greater chance of creating new DNA
words that can be bound by regulator proteins and bring about new
gene regulation in genomes like ours. That’s why changes in gene
regulation have been crucial to the evolution of large and complex
organisms –perhaps more so than changes in genes themselves”

59. “The genome of a multicellular organism resembles the
workshop of an inventor, filled to the rafters with spare parts,
tools, abandoned projects, disassembled machines, and half-
finished designs –in short, the kind of junk that is the seed of
the next breakthrough invention”

60. “The two plateaus in the flat
plane become a circular
ridgeline easily circumnavigated
by a population propelled only
by a modest amount of genetic
drift”

61. “A paltry three dimensions fail us when we try to
understand the ability to bypass fitness valleys”

62. “Something profound about the architecture of
multidimensional adaptive landscapes: a peak is
usually not a single location, but more like a network
of high-altitude paths that form a sprawling spiderweb
extending far through the landscape”

63. “The peculiar architecture of adaptive landscapes
where each peak really is a network of multi-
dimensional ridges, helps evolution solve difficult
problems”

64. “Along this network, diverse forms of regulation
and metabolism can co-exist. They are each able
to build and maintain an optimally functioning
body but do so in different ways”

65. “A child’s genome differs from that of its parents by
some 1.5 million letters, or 0.05% of its genome. This
may not sounds like much, but adaptive landscapes
help us grasp its true magnitude”

66. “If a single step on a landscape –a single letter change
in a genome- covered a human step, then child-parent
genome swapping teleports a child about 700 miles in
a single leap”

67. “The more two parents differ in their DNA, the further
recombination can leap, and the greater its creative
powers can become… Hybridisation can also be very
successful. It can even launch entirely new species”

68. “Recombination is much more likely to preserve life –
up to thousands of times more- than random mutation
is. There is no match for recombination’s enormous
creative potential”

69. “Genetic drift, DNA recombination and the sprawl of
adaptive ridges counterbalance natural selection’s
short-sightedness”