Transcript Evolution in Action

Evolution in Action
Startling conclusions on the ultimate
consequences of unsupervised tinkering
The Evolutionary Algorithm
• Start with something that works pretty well.
• Make tweaked copies of it.
• Various copies compete against each other,
and environment. ‘Fittest’ reproduce most.
• Repeat on large populations for billions of
years.
• Ultimate source of the intelligence in the
genome.
• A very slow way to develop software.
Double Helix
• DNA is composed of the
bases A,C,G and T
• A and T always pair, C
and G always pair
• Each strand can serve as
a template for the other.
Mutation and DNA
• Radiation can break DNA.
• Aromatic chemicals can nestle between
bases and cause insertions when copying
• Other chemicals like AZT mimic bases,
cause substitutions.
• UV light can fuse pairs of T’s
• Copy mechanism is only 99.9999999%
perfect.
Viruses
• Some viruses integrate their genome into
genome. HIV is an example.
• When a virus leaves a cell it can accidently
pick up some of host DNA, transporting it
to another host.
• Occasionally viruses can transport DNA
from one species to another.
Transposons
• “Selfish” DNA. Stripped down viruses.
• Make copies of themselves which are
randomly inserted into genome.
• Some end up making partial copies of other
genes as well.
• Currently relics of transposons make up half
of human genome.
Sex
• Each individual has two copies of each
chromosome, one from mom, one from dad.
• Sperm/egg have only one copy of each
chromosome, chosen randomly.
• Chromosomes ‘cross over’ in at least two
places further shuffling genes.
• Cross-over between different copies of
same transposon can cause large
duplications, deletions.
Crossing Over
Normal crossover:
homologous regions
swapped.
Crossover seeded by repeat:
leaves one chromosome with a
large insert, the other with a large
deletion.
Advantages of Sex
• Allows selection to more easily work on
combinations of traits.
• Allows genome of species to carry significantly
more information than genome of an individual.
• Encourages fruitful collaborations.
• Asexually producing species often thrive for a
time, but are slower to adapt to change.
• Many organisms only reproduce sexually only in
times of stress, reproduce asexually normally.
The Value of Duplications
• Each gene has an important function. Most
mutations disrupt this function.
• Duplication of a gene frees one copy to
evolve another function.
• Clusters of related genes are the fastest
evolving part of the genome.
Human
vs.
Human
• A variation every 1000 nucleotides.
• 90% of human variation is within African
populations.
• There are enough humans, and the mutation rate is
high enough, that on average each base is mutated
several times in each generation.
• Humans each carry hundreds of bad mutations.
Most are recessive, only show up with inbreeding.
Human vs. Chimpanzee
• A difference every 100 bases.
• A new transposon every 50000 bases
• Two chromosome in one species fused
compared to the other.
Human vs. Mouse
• In general 40% of bases have changed.
• In functional regions only 15% of bases have
changed.
• Looking for conserved regions between human
and mouse helps identify functional parts of
human genome.
Evolution of Multicellular Life
• Competition between cells is intense.
• Cells dividing randomly form a solid ball.
Cells in the middle of ball get starved
• Beginnings of multicellular forms were
cells dividing in organized fashion to form
filaments, sheets or hollow balls.
A Filamentous Form
Anabaena - a filamentous algae. Filamentous forms have
evolved independently many times.
A Hollow Ball
Volvox - an algae that forms hollow balls. Baby volvos
are forming inside. The hollow ball is more rare than
filaments, but human embryos go through this stage.
Building a Body from DNA
• 3 billion bases of human DNA contain
roughly 30,000 genes.
• The products of the genes are the parts that
make up a cell.
• These genes are turned on and off in a very
intricate fashion to form and maintain a
human body.
• Some genes regulate other genes.
How DNA is Used by the Cell
Promoter Tells Where to Begin
Different promoters activate different genes in
different parts of the body.
A Computer in Soup
Idealized promoter for a gene involved in making hair.
Proteins that bind to specific DNA sequences in the
promoter region together turn a gene on or off. These
proteins are themselves regulated by their own promoters
leading to a gene regulatory network with many of the
same properties as a neural network.
Evolution of Cancer
• Human body has 1014 cells descended from a
single egg cell.
• Many mutations occur in cells over your lifetime.
• Mutations that favor growth of an individual cell
over growth of the organism lead to cancer.
• A half-dozen genes must be disabled to have a full
fledged malignant cancer.
• Cancer cells have mutations that encourage
mutation – flawed DNA repair mechanisms.
• Radiation paradoxically induces cancer and cures
it.
The Peculiar Dangers of Smoking
• Smoking kills lung lining rapidly. Lung
cells must reproduce a lot to keep up.
• Many opportunities for copying errors and
growth competition.
• Aromatic compounds in ‘tars’ intercalate in
DNA leading to frame shift errors.
• Tobacco accumulates uranium, leads to
ionizing radiation and chromosome breaks.
Engineering vs. Nature
• Disadvantages of Nature
– Blind forces of mutation cause 100 problems
for every benefit. Worse than a bad hacker!
– Genome is cleaned up by pain of infertility,
spontanious abortion, and disease.
• Advantages of Nature
– Nature just runs each experiment on a few
organisms.
– It’s taken 3 billion years, but Nature has
accumulated great wisdom.
Startling Conclusions
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Evolution good
Homogeneity bad
Sex good
Inbreeding bad
Cooperation good
Smoking bad
The body is built from a 1 dimensional code.
Genetic engineering is best practiced a small scale
The End