CCC Lecture 2 2014 Life, Evolution, Selection and Synthesis.pdf

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

CCC Lecture 2 2014 Life, Evolution, Selection and Synthesis.pdf

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