The Origin and Classification of Life Classification and Evolution of Organisms.
The Origin of Life Evolution
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Transcript of The Origin of Life Evolution
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Frederick H. Willeboordse
Natures Monte Carlo Bakery:
The Story ofLife as a Complex System
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The Origin of Life
Lecture 8 Clearly, we are alive. But when
did life start and where? What
can we say about the origin of
life?
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Experiments and Theories
Stages of prebiotic evolution
How did the earths crust and
atmosphere look like when life
originated?
How can the building blocks of life
(nucleotides, amino acids) be synthesized?
These blocks may (partially) have been
different from modern blocks.
How did the building blocks organize into
living organisms?
Reasonably wellunderstood.
Poorly
understood.
Geophysical Stage
Chemical Stage
Biological Stage
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Time-line
Stages
4.4 4.2 3.6 3.44.0 3.8
Earth
Formation
Stabilization
of
Hydrosphere
Fewer Meteorite
Impacts
Organic Matter
from
living organisms
Earliest
Fossils
Origin of LifeRNA World?
Billion
years ago
Geophysical Stage
Chemical Stage
Biological Stage
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Formation of
the earth
Oldest minerals
Isua rocks
Apex fossils Rise of O2
Multi-cellular
fossilsAnimal
fossils
Geophysical Stage
CO2 -N2 atmosphere O2 -N2 atmosphere
4.0 3.0 1.0 0.02.0
Time-line
Chemical Stage
Biological Stage
Evolution of Life
Humans
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Geophysical Stage
Atmosphere
Composition of first Atmosphere (~4.5 billion years ago)
After the earth began forming, due to gravitational forces, the heavier
elements moved towards the center and the lighter elements moved
outwards forming a first atmosphere.The composition of this atmosphere is quite well known since we know the
composition of the materials that formed earth. It was reducing (i.e. it
removing oxygen in chemical reactions) containing H2 and CH4 but lost to
space due to heat and the planets small size. What was left was a more or
less barren rock (without oceans either).
Old rocks show that the earth
had a neutral atmosphere
from 3.8 to 2 billion years
ago.
There is a lack of Neon gas in the
atmosphere which is abundant among the
original gasses.
This implies that the atmosphere is likely
generated by volcanic activity.
2 pieces of solid evidence for loss of first atmosphere
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Geophysical stage
Under immense gravitational pressure and due to radioactive
decay, the interior of the planet melted driving out gasses
through volcanic action.
The gasses released through volcanoes formed the initial
components of the current atmosphere and was likely very
similar to the gasses still escaping from volcanoes nowadays.
Geophysical Stage
H2O, CO, CO2, CH4, NH3, N2, H2S, H2
Most of the early earths water was probably in vaporous
form leading to intense rains while the oceans were slowly
forming.
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Geophysical Stage
Atmosphere
Plenty of water steam to start with.
Non reducing atmosphere, no H2, except high up from photolysis of H2O. No oxygen in the atmosphere.
CO2 gas massive amounts
N2 gas about same as present
Little H2S from volcanic activity
Clouds of volcanic ash; sulphate (SO42- ) materials.
Composition of second Atmosphere (~4.4 billion years ago)
Cyanide (HCN) and formaldehyde (H2CO) were readily formed
from the volcanic gasses.
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Geophysical Stage
Oceans
Neutrals like H2O, CO2, N2
Ferrous ions like Fe2+
. The color of the ocean was different being greenishyellow!
ydrothermal vent water contained H2S
SO42- is the main sulphur compound in seawater
Other ions like Na+, Cl-, PO43-
Composition of the Oceans(~4.2 Billion years ago)
The oxygen in sulphate came from water, there was no
dissolved oxygen in ocean.
Phosphate PO43- is important for biochemistry but has very low
concentration in sea water.
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Geophysical Stage
Physical Conditions
How did our planet look(~4.2 Billion years ago)
Weak sun, no ozone later, no shielding from UV Radiation.
Faster rotation with about 15 hours in a day. Turbulence. High winds, big ocean waves. Earth-moon distance only 2/3 of todays. Much higher tides
(perhaps up to 30m). Average surface heat flow 3 times greater. Therefore a lot of
hydrothermal cooling.
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Experiments
Chemical Stage
There are two very famous experiments. But
we now know that they are inapplicable as
they wrongly assume a reducing atmosphere
for the time when life likely originated.
Stanley Miller
Juan Or
Mechanism for creating
Amino Acids
Mechanism for creating
Nucleotides
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Amino Acids - Stanley Miller
In a reducing environment, amino acids
are easy to synthesize from naturally
occurring molecules.
The experiments fail in a neutral oroxygen-rich atmosphere.
methane
hydrogen
ammonia
water + Amino Acid
?
reducing atmosphere
Ocean
Atmosphere
So the good news is amino acids can be synthesized, the bad
news is that we now know that the atmosphere was not reducing.
Chemical Stage
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Nucleotides - Juan Or
Experiment by Or
Phosphate ionOccurs naturally
Recall:
Nucleotides have 3 parts
HC
C
C
C
O
OH
1
23
4
OCH25
H
HHH
O-
O-
P
O
HCN
C
N
C
HC
O
NH2
C
SugarCan be synthesized from naturally occurring
formaldehyde the problem is though that
the concentration needs to be high.
Nitrogenous Base
Chemical Stage
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Ammonia +
Hydrogen cyanide + Organic base
(adenine)
Take ammonium cyanide and let it stand. In a reducing
environment ammonium cyanide can occur naturally but in an
oxygen-rich atmosphere it will react.
reducing atmosphere
Nucleotides - Juan Or
So the good news is that a base for a nucleotide can be found, the
bad news is again that we now know that the atmosphere was not
reducing.
Chemical Stage
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Oro-type reactions might also have been possible with the direct
products of volcanic gasses.
Possible synthesis of an amino acid a-la Or
HCN
HCNHCNHCNHCN
C
CN
CH
N
C
NH
N
HC
NH2
Adenine
A
Hydrogen Cyanide
Nucleotides - Juan Or
Chemical Stage
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Hence all the three parts of nucleotides can occur
naturally in a reducing environment.
However, getting the parts to combine into a stable nucleotide
is more of a problem.
For random combinations only about 1% is such that the
molecule is stereo-chemically correct.
Individual nucleotides quickly hydrolyze back into their
components.
Nucleotides - Juan Or
Chemical Stage
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Chemical Stage
Land
Very little land!
However, there was much less land4 billion years agothan there is now!
Perhaps it would be better to look for the origin of life
in the ocean.
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Vents
Hydrothermal
Vents, Crust
However, the earth is more than just
its atmosphere. It could be that life
originated in the crust or on the
ocean-floor near hydrothermal vents.
Hydrothermal vents:
Lots of life, reducing
environment
If this is correct life could have originated on several planets/moons in our solar system.
4 important discoveries
Bacteria that bear no
resemblance to other
species exist deep
underground
Gelatinous bubbles
can be formed in vent-
like situations where
hot water enters cold
water
Ancient bacteria
seem to be
theromophilic
Chemical Stage
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Vents
Total length of ridges where
one can find the vents:
~ 75,000km
Chemical Stage
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Vents
There are many lithotrophic
prokaryotes that can live on a
plain diet of inorganic
nutrients. These may get their
carbon from CO2 and their
energy from e.g. H2S.
Experiments
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Vents
Hydrothermal Vents are full of
life!
Experiments
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Evidence
Genetic evidence The genetic apparatus is universal and henceit is likely that all modern cells share a
common ancestor.
When this ancestor lived cannot bedetermined though.
Microfossils can show that life probably existed
since around 4 billion years ago.
However, it is unclear when modern cells
evolved.
Paleontological evidence
Biological Stage
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Theories
Biological Stage
There are several leading theories though
unfortunately none of them supported by
clear evidence at this moment.
Manfred Eigen
Cairns-Smith
RNA World
Clay
Freeman Dyson Double Origin
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John von Neumann
Observed that replication and metabolism are
logically separable.
Introduced analogy between automata and
living organisms
made the distinction between what is now
called software and hardware.
Theories
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Manfred Eigen
Genes Enzymes Cells
He believes that life started with RNA. It incorporates detailed
knowledge about genes.
RNA World
1. Eigen showed that
RNA can replicate
without a template
This theory is popular for three main reasons.
2. RNA can act as
enzyme.
3. DNA is structurally
simpler than enzymes.
Theories
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&Quasi Species Hypercyles
There are two key concepts:
A quasi species is a population of
related but not identical RNA
molecules. The molecules can
replicate but only in an imperfect
way. Nevertheless, overall somestructure is preserved.
A hypercycle is the interaction
between several quasi species
where enzymes associated with
one quasi species assist in the
replication of another quasispecies.
Theories
Manfred Eigen
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Eigen was of course aware of this but he thought it was
manageable. Unfortunately, later on, extensive computer
simulations of Eigens ideas revealed:
Problems
A replicative (as opposed to a
reproductive) apparatus needs to
function almost perfectly in order to
function at all.
Otherwise errors will accumulate
leading to an error catastrophe.
Theories
Manfred Eigen
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There are three more types of catastrophes!
Selfish RNA
Short Circuit
Population Collapse
One type of RNA starts to
replicate faster than therest while stopping to act
as a catalyst. As a
consequence, the other
RNA species are squeezed
out.
One type of RNA starts tocatalyze a later stage in the
hypercycle cutting out one
or more stages.
If the population of an
essential RNA molecule in
the hypercycle drops tozero, the whole cycle will
collapse.
More Problems
Theories
Manfred Eigen
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Main Success
Demonstrated that nucleotide monomers can give rise
to nucleic acid polymers that replicate and mutate(without providing an RNA template).
In Eigens experiments, an enzyme was necessarybut this could not have existed on the early earth.
Main Problem
Theories
Manfred Eigen
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Leslie Orgel
Showed that nucleotide monomers can polymerize into
RNA given a suitable template (without the help of an
enzyme). I.e. copying can occur spontaneously under the
right conditions.
Since Orgel depends on a template, his experiment too is
not sufficient to indicate how life could have started.
After all where did the template come from?
Theories
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Alexander I. Oparin
Cells Enzymes Genes
Oily liquid in water leads to coacervates.
These can contain random molecular populations which are later
organized by enzymes.
The theory dates back to 1924 and hence did not take our modern
knowledge of genes into account. It is a theory that starts with
metabolism.
Order of events in the origin of life:
Theories
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Oparin
Under the right conditions, colloids of macro-molecules give
rise to so-called coacervate droplets.
Hydrophobic (parts of) macro-molecules
are surrounded and stabilized by a shell of
water molecules.
An example are the phospholipids that
can form vesicles.
Theories
Coacervates
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Garbage-bag world
Bags contain random collections of
molecules
A somewhat modernized version of Oparins theory
by Doron Lancet.
Initially, there will be some form ofreproduction but it will take a (long)
time for replication to be established.
Theories
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Garbage-bagworld
Theories
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Oparin
While in principle, this theory is not very sensitive to errors,
how a garbage-bag can lead to life is less clear.
As a first step one would need some
form of autocatalytic cycle. There would
also need to be a mechanism for the
vesicle/droplet to grow and eventually
split.
How RNA entered the picture is further unclear.
Theories
Problems
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Cairns-Smith
Micro-crystals of clay contain metal ions that can function as
information carries.
CellsEnzymes GenesClay
The metals could catalyze reactions according to their arrangement and thus the crystal might
perform a function similar to RNA.
Clay crystals (like most crystals) could even grow and then be split (e.g. by the forces of
nature) thus replicating themselves.Eventually, the replicative apparatus is replaced by the more efficient RNA.
Theories
This seems to be rather far-fetched.
but one never knows of course!
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Nucleic acids are the oldest parasites that
did the Eigen experiment inside the cell dueto the natural presence of the nucleotides
and the cells enzymes (in that sense RNA
was a parasitic disease).
Theories
Freeman Dyson
Double origin hypothesis. This is quite close to Oparin but has
RNA as a parasitic invader.
Believes that original cells were metabolic that couldreproduce but not replicate.
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Dyson - Strengths
* Hardware comes before
software
* Experimentally testable
However, what is really hardware? If one
gets the analogy wrong
Seems to be the case
Is also true for Eigens ideas
* Amino Acids are easier tomake than Nucleic Acids
Theories
Dyson - Problems
Basically the same as for Oparin.
Furthermore: Where does the invading RNA come from?
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Sustaining Life
After life somehow originated, how did it sustain itself?
Evolution
We know that it evolved but by what mechanisms and (though
there is no answer to that), are these mechanisms a necessity ofa general universal biology?
Genetic Drift
Natural Selection
Explores
Fills Niches
Extinctions Makes Room
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Genetic Drift
Early on in evolution, genetic drift may have been more important
than natural selection if (when?) there was no genetic apparatus
since this would imply fairly large error rates.
Genetic drift implies that random statistical fluctuations are the
key driving forces of change and evolution.
Evolution
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Natural Selection
Natural selection as such does not imply that organisms need to
become more complex.
The process in nature by which, according to Darwin's theory of
evolution, only the organisms best adapted to their environment
tend to survive and transmit their genetic characteristics in
increasing numbers to succeeding generations while those less
adapted tend to be eliminated.(Source: The American Heritage Dictionary of the English Language, Fourth Edition)
Evolution
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1. Field of bullets: random extinction without regard to differences in
fitness Opens possibilities for new development
2. Fair game: selective extinction in a Darwinian sense, leading to the
survival of the most fit or best adapted species Niches become
increasingly unavailable
3. Wanton extinction: selective extinction, where some kinds of
organisms survive preferentially but not because they are better
adapted to their normal environment. I.e. Systematic extinction ofgroups not based on their fitness but on some other factor (e.g.,
body mass, favored habitat, etc.) Groups of less fit survive,
more fit perish; Clears out niches for new evolutionary thrust
Extinctions
Major types
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Number of plays
Gamblers stake
Extinctions
Game with even-odds and an adsorbing boundary at zero. You
flip a coin H win, T lose.
When you reach the adsorbing boundary you are extinct in
money and cannot play again.
Power of chance
Similar results can be had in this
kind of scenario
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Gambling for survivalA long lived species is like having a long run of good luck at the casino.
Species extinction weakens the future of the genus.
Speciation protects the genus.
A large number of species means temporary protection from extinction.
There are 1700 species of rodents today, greater than any other order of living
mammals.
There are nine hundred species of bats.
Almost two thirds of all living mammal species are either rodents or bats.
How have rodents & bats avoided early extinction?
Extinctions
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Bacteria
Archaea
Eucaryotes
Last common ancestor
Cells with primitive,
unregulated ATP synthetases
& protein synthesis
DNA genome
Protein synthesis
RNA world
Pre-biotic soup
The Three Domains of Life on Earth
Evolution
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Smallest bacterial genomes:
Mycoplasma species 585 1330 kbp
Spirochaete species 900 ? kbp Smallest archaeabacterium is
methanobacterium thermautotrophicum 1623 kbp.
Kbp = thousand base pairs
It is speculated that 318 562 kbp may represent the
border line between the living & non living (zombie?)
organism.
Minimal Genome Size Needed for Life
Genome size
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A parasite in a wide range of hosts (humans, animals, insects, plants). It is
an anaerobe that ferments glucose perhaps other sugars by way of glycosis
to lactate and acetate.
It has no cell wall.
It has a circular genome (DNA is a circular polymer molecule).
It has the smallest genome of any living system sequenced so far.
Genome has 470 coding regions including key genes for life: DNA
(replication, transcription, translation, repair), cellular transport & energy
metabolism.
MG has DNA weighing 580.070 kbp.DNA has a low G+C content.
Mycoplasma genitalium
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The origin of life is still far form clear!
Life may have started in a garbage-bag (Oparin) or with an RNA
world (Eigen). Both these theories assume a single origin.
Dyson combines the two to formulate
a double-origin hypothesis where
RNA invades reproducing garbage-
bags.
Did life start here?
Wrapping up
Key Points of the Day
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The Cell, Alberts et al
Origin of Life, Freeman Dyson
The Origins of Life, John Maynard-Smith and Eors Szathmary
Dive and Discover
Wrapping up
Give it some thought
References
Where did life originate?
http://www.divediscover.whoi.edu/http://www.divediscover.whoi.edu/