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8/9/2019 CCC Lecture 2 2014 Life, Evolution, Selection and Synthesis.pdf
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Lecture 2, 29th January 2014
Life, Evolution, Selection and Synthesis
Life 2.0: Synthetic Biology and the FutureBioeconomy
Dr. Julian A. Tanner,[email protected]
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Venters synthetic cells
Is it really life? - What is life?
A central question of philosophy and science.
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Raphael the School of Athens (painted 1509 as a fresco
in the Popes personal library in the Vatican)
PythagorasAnaximander Plato Aristotle
(Allow some artistic license! These philosophers did not live at same time!)
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Origins of Scientific Thought as Applied to
Understanding Life
Thales - developed the scientific approach,predicting an eclipse in 585 BC in city of Miletus,
Ionia (~630-560 BC)
The Greeks were the first to use material
principles rather than superstition or religion tounderstand the natural world.
Anaximander (610-546 BC) first to investigate
fossils, proposed animals sprang from sea.
Portrayal of Anaximander in
Raphael's painting The School of
Athens.
At first human beings arose in the inside
of fishes, and after having been reared like
sharks, and become capable of protectingthemselves, they were finally cast ashore
and took to land. Plut Symp.
Quaest, 730 f (R. P. 22.).
(!!)
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First thoughts on li fe developed in port ci ty of Miletus by Anaximander
But critically its geography was excellent for fossils
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Miletus, Ionia (ruins now in
modern-day Turkey), thecradle of scientific thought -
now ruins in a rural area
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Anaximander: proposed world once covered in water, with plants and
animals arising from mud.
Taoist thought: world from a formless void.
Hebrew thought: similar.
Curious Similarities of Ideas of Origins of Life across Cultures 2500 years ago
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Xenophanes (575-450 BC) used fossils to conclude a
changing earth
Xenophanes linked fossils to changing
earth. Earth has history.
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Herodotus and Hippocrates
Herodotus (484-425 B.C.E.)"the backbones and ribs of suchserpents as it is impossible todescribe: of the ribs there werea multitude of heaps. . . "
Hippocrates 460-357 BC
fossils found in excavations ofhis medical school Asklepieion.
Hippocrates Medical School on Kos in Greece
550 BC Hercules
killing a monster
(dinosaur?)
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Plato (427-343 BC)
Platos opinion was that variation in organisms in our
world is because imperfect copies of real types in the
real world incorporated into Christianity.
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Aristotle, a great natural historian
Incredibly detailed
observations on
cuttlefish, octopus.
Split animals into two
types, those with blood
and those without. Rembrandt (1653): Aristotlecontemplating a bust ofHomer . Metropolitan
Museum of Art, New York.
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History of Ancient Evolutionary
thought in China Taoist philosophy. "Probe into the mystery of
heaven and earth and understand the root of
creation" (The Taoist Canon, , ~400AD)
Shen Guo (1031-1095, Song dynastypolymath)
(pseudonym Mengxi Weng )
Significant work on fossilized bamboo, fossils,sedimentary deposition with strata of fossils
predated James Huttons work of 1802 byalmost 800 years.
Bamboo and rocks byLi Kan (12441320)
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The Rediscovery of Aristotle
Fused and reconciled with Christian doctrineinto a philosophical system known as
Scholasticism.
But impeded observational science. Doctrinebased, not experimental.
Many errors never retested: attributed heart
to mental thoughts, women colder than menand thus lower life form and mud generatedinsects.
Da Vincis Vetruvian Man, strongly
influenced by Renaissance discovery of
Aristotle
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The Greek
Philosophers
600-300 BC
The Romans from 200 BC-200AD
Taoist philosophy
Shen Kuo 11th Century
Linnaeus 1707-1778
Buffon 1707-1788
Darwin 1809-1892
Thomas Malthus 1776-1834
Louis Pasteur 1822-1895
Jean-Baptiste Lamarck 1744-1829
Alexander Oparin 1894-1980
James Watson 1928
Francis Crick 1916-2004
Craig Venter 1946-
Stephen Jay Gould 1941-2002
Richard Dawkins 1941-
Overview of Important Thinkers on Life and Evolution Discussed in this Course
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Carl Linnaeus 1707-1778 Swedish botanist, the father of
modern taxonomy
Invented the bionomial nomenclaturefor organisms (e.g., Homo sapiens,Taraxacum officinale).
Systema Naturae classified 4,400species of animals and 7,700 speciesof plants.
First to place humans in biologicalclassification system.
But believed species fixed.
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Jean-Baptiste Lamarck (1744-1829)
His viewpoints (later proven flawed):
Nature tends to increase the size of
living individuals to a predetermined
limit
The production of a new organ
results from a new need
The development reached by organsis directly proportional to the extent
to which they are used
Everything acquired by the individualis transmitted to its offspring
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Lamarcks Examples he used for
Argument
The mole lost eyes because
of no use??
Aquatic bird constant
stretching of skin led to
webbed feet??
Giraffe neck
stretched via
generations of
ancestors stretchingthem??
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Darwin (1809-1882) Theory of Evolution
In any generation, not all individuals of
the same species succeed in reproducing
Members of a species are not identical,
they exhibit individual variation
Apart from variation due to
environmental differences, themajority is inherited and transmitted
from parents to offspring
Reproductive success is not random.It is associated with inherited
characteristics, some of which will be
more beneficial in particular
circumstances than others
Darwin's first sketch of an
evolutionary tree from his First
Notebook on Transmutation of
Species (1837)
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1859 Origin of Species by Charles
Darwin
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Lamarck v Darwin Lamarcks theory required adaptation to create new
variations This was followed by the inheritance of these
characteristics
Darwins theory requires random hereditary variation
first, followed by selection of the variations
The argument was over when Mendels laws of genetics
were rediscovered at the end of the 19th century
Variations are due to hereditary traits passing from onegeneration to the next in predictable frequencies
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Video on Darwin and his life
http://www.pbs.org/wgbh/evolution/educators/teachstuds/svideos.html
Other resources for student to follow-up in self-study
http://www.pbs.org/wgbh/nova/beta/evolutio
n/big-thinkers-evolution.html
OK, but why is evolution important for synthetic biology?
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This led him to the idea of natural
selection.
Natural selection rests on three indisputable facts:
Organisms produce more offspring than can survive.
Individuals vary in their characteristics.
Many characteristics are inherited by offspring from
their parents.
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It follows logically that
Some individuals will be better suited to their
environment - they will survive and reproduce moresuccessfully than individuals without those characteristics.
Future generations will thus contain more genes from
better-suited individuals.
As a result, characteristics will evolve over time to
resemble those of the better-suited ancestors.
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Artificial Selection - Darwins hopeful
monstersThe circumstances under which
our domestic productions are
reared are widely different. . . In
conformity with this, all our
domesticated productions, with
the rarest exceptions, vary far
more than natural species.-Darwin (1896)
Wilner (2006) views Darwins use of monstrous
in an experimental sense. Darwins monstrous
refers to the degree of artificiality in the breeders
experiment. Experiments uncover the nature of
the elements, often with very artificial treatments.
Darwin and fancy pigeons
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Darwin and fancy pigeons
Secord 1981
Analogy between artificial andnatural selection central to the
Origin
If humans can produce such
divergent phenotypes in short
time periods through selection
(as in pigeons) wouldnt nature
be able to produce the same
over millions of years of natural
selection?
Darwin discusses products of
domestication: cows, rabbits,sheep
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English carrier pigeon Runt pigeon
Jacobin pigeon
hundreds of pigeon breeds
Pouter
pigeon
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Dogs even more variety.
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Tulips even more.
Candidate genes in domestication
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Candidate genes in domestication
Signatures of positive selection show the a
cauliflowergene carrying a nonsense mutation issegregating in broccoli, wild cabbage, kale, and
cauliflower. A floral regulatory locus. Most of the
genomes are identical.
Many genes implicated in domestication are shown to be
involved in gene regulation or in regulatory regions
themselves. Does this follow a similar pattern to natural
systems?
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Convergent evolution in dog domestication
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Dogs can read humancommunicative gestures
(ie.pointing) better in comparison
than wolves
Unclear if this ability is a result of
direct selection or a by-product of
selection against fear and
aggression towards humans
Experimental population of fox kits
bred over 45 years to approach
humans fearlessly and non-aggressively
As skillful as dog puppies in
human gestures and more skillfulthan a second control population of
fox kits
Convergent evolution in dog domestication
http://www.youtube.com/watch?v=enrLSfxTqZ0
http://www.youtube.com/watch?v=oDb27ZP9zEE&feature=related
?
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So why does this matter for synthetic biology?
From Synthia, we dont necessarily need to know all the exact
biochemistry to activate a pathway. Similar to Darwin, we could use
artificial selection towards traits we need.the new primal
ancestor?
Bacteria that turn
waste to energy?Bacteria for food
generation? Bacteria for medical
application?
Limitless
potential
application?
Artificial selection as possible mechanism