Download The Origin of Life - Frederick H. Willeboordse

Nature’s Monte Carlo Bakery:
The Story of Life as a Complex System
GEK1530
Frederick H. Willeboordse
[email protected]
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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
Geophysical Stage
Chemical Stage
Biological Stage
How did the earth’s 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 well
understood.
Poorly
understood.
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Time-line
Stages
Origin of Life
RNA World?
Earth
Formation
Billion
years ago
4.4
Stabilization
of
Hydrosphere
Fewer Meteorite
Impacts
4.2
4.0
Organic Matter
from
living organisms
3.8
Earliest
Fossils
3.6
3.4
Geophysical Stage
Chemical Stage
Biological Stage
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Time-line
Evolution of Life
CO2 -N2 atmosphere
O2 -N2 atmosphere
Geophysical Stage
Chemical Stage
Biological Stage
Oldest minerals
Humans
Multi-cellular
fossils
Rise of O2
Isua rocks
Apex fossils
4.0
3.0
2.0
1.0
Animal
fossils
0.0
Formation of
the earth
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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 planet’s small size. What was left was a more or
less barren rock (without oceans either).
2 pieces of solid evidence for loss of first atmosphere
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.
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Geophysical Stage
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.
H2O, CO, CO2, CH4, NH3, N2, H2S, H2
Most of the early earth’s water was probably in vaporous form
leading to intense rains while the oceans were slowly forming.
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Geophysical Stage
Atmosphere
Composition of second Atmosphere (~4.4 billion years ago)
• 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.
Cyanide (HCN) and formaldehyde (H2CO) were readily formed
from the volcanic gasses.
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Geophysical Stage
Oceans
Composition of the Oceans (~4.2 Billion years ago)
• Neutrals like H2O, CO2, N2
• Ferrous ions like Fe2+ . The color of the ocean was different being
greenish yellow!
 Hydrothermal vent water contained H2S
• SO42- is the main sulphur compound in seawater
• Other ions like Na+, Cl-, PO4 3-
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 today’s. Much higher tides
(perhaps up to 30m).
• Average surface heat flow 3 times greater. Therefore a lot of
hydrothermal cooling.
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Chemical Stage
Experiments
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
Mechanism for creating
Amino Acids
Juan Oró
Mechanism for creating
Nucleotides
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Chemical Stage
Amino Acids - Stanley Miller
In a reducing environment, amino acids
are easy to synthesize from naturally
occurring molecules.
The experiments fail in a neutral or
oxygen-rich atmosphere.
hydrogen
water
methane
ammonia
+
Amino Acid
?
‘Atmosphere’
‘Ocean’
reducing 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.
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Chemical Stage
Nucleotides - Juan Oró
NH2
Recall:
Nucleotides have 3 parts
Nitrogenous Base
C
HC
N
Experiment by Oró
C
O
C
HC
O- P OCH
2
5’
O
N
O
O
C
C 1’
4’
H
HH
H
Sugar
C
C 3’
2’
Can be synthesized from naturally occurring
Phosphate ion
formaldehyde – the problem is though that
H
OH
Occurs naturally
the concentration needs to be high.
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Chemical Stage
Nucleotides - Juan Oró
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.
Ammonia +
Hydrogen cyanide
+
Organic base
(adenine)
reducing atmosphere
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.
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Chemical Stage
Nucleotides - Juan Oró
Oro-type reactions might also have been possible with the direct
products of volcanic gasses.
Possible synthesis of an amino acid a-la Oró
HCN
HCN
HCN
HCN
HCN
N
NH2
C
C
N
A
HC
NH
C
CH
N
Adenine
Hydrogen Cyanide
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Chemical Stage
Nucleotides - Juan Oró
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.
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Chemical Stage
Land
However, there was much less land 4 billion years ago
than there is now!
Perhaps it would be better to look for the origin of life
in the ocean.
Very little land!
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Chemical Stage
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.
4 important discoveries
Hydrothermal vents:
Lots of life, reducing Bacteria that bear no
environment
resemblance to other
species exist deep
underground
Gelatinous bubbles
can be formed in vent- Ancient bacteria
seem to be
like situations where
theromophilic
hot water enters cold
water
If this is correct life could have originated on several planets/moons in our solar system.
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Chemical Stage
Vents
Total length of ridges where
one can find the vents:
~ 75,000km
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Experiments
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.
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Experiments
Vents
Hydrothermal Vents are full of
life!
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Biological Stage
Evidence
Genetic evidence
The genetic apparatus is universal and hence
it is likely that all modern cells share a
common ancestor.
When this ancestor lived cannot be
determined though.
Paleontological evidence
Microfossils can show that life probably existed
since around 4 billion years ago.
However, it is unclear when modern cells
evolved.
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Biological Stage
Theories
There are several leading theories though
unfortunately none of them supported by
clear evidence at this moment.
Manfred Eigen
RNA World
Cairns-Smith
Clay
Freeman Dyson
Double Origin
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Theories
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.
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Theories
Manfred Eigen
He believes that life started with RNA. It incorporates detailed
knowledge about genes.
Genes
Enzymes
Cells
RNA World
This theory is popular for three main reasons.
1. Eigen showed that
RNA can replicate
without a template
2. RNA can act as
enzyme.
3. DNA is structurally
simpler than enzymes.
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Theories
Manfred Eigen
There are two key concepts:
Quasi Species & Hypercyles
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 some
structure is preserved.
A hypercycle is the interaction
between several quasi species
where enzymes associated with
one quasi species assist in the
replication of another quasi
species.
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Theories
Manfred Eigen
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’.
Eigen was of course aware of this but he thought it was
manageable. Unfortunately, later on, extensive computer
simulations of Eigen’s ideas revealed:
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Theories
Manfred Eigen
More Problems
There are three more types of catastrophes!
Population Collapse
Selfish RNA
Short Circuit
One type of RNA starts to
replicate faster than the
rest while stopping to act
as a catalyst. As a
consequence, the other
RNA species are squeezed
out.
One type of RNA starts to
catalyze a later stage in the
hypercycle cutting out one
or more stages.
If the population of an
essential RNA molecule in
the hypercycle drops to
zero, the whole cycle will
collapse.
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Theories
Manfred Eigen
Main Success
•
Demonstrated that nucleotide monomers can give rise
to nucleic acid polymers that replicate and mutate
(without providing an RNA template).
Main Problem
•
In Eigen’s experiments, an enzyme was necessary
but this could not have existed on the early earth.
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Theories
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?
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Theories
Alexander I. Oparin
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:
Cells
Enzymes
Genes
Oily liquid in water leads to coacervates.
These can contain random molecular populations which are later
organized by enzymes.
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Theories
Oparin
Coacervates
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.
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Theories
Garbage-bag world
A somewhat modernized version of Oparin’s theory
by Doron Lancet.
‘Bags’ contain random collections of
molecules…
Initially, there will be some form of
reproduction but it will take a (long)
time for replication to be established.
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Theories
Garbage-bag
world
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Theories
Oparin
Problems
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.
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Theories
Cairns-Smith
Micro-crystals of clay contain metal ions that can function as
information carries.
Clay
Enzymes
Cells
Genes
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.
This seems to be rather far-fetched….
… but one never knows of course!
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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 could
reproduce but not replicate.
• Nucleic acids are the oldest parasites that
did the Eigen experiment inside the cell due
to the natural presence of the nucleotides
and the cells’ enzymes (in that sense RNA
was a parasitic disease).
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Theories
Dyson - Strengths
* Hardware comes before
software
However, what is really hardware? If one
gets the analogy wrong …
* Amino Acids are easier to
make than Nucleic Acids
Seems to be the case
* Experimentally testable
Is also true for Eigen’s ideas
Dyson - Problems
Basically the same as for Oparin.
Furthermore:
Where does the invading RNA come from?
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Evolution
Sustaining Life
After life somehow originated, how did it sustain itself?
We know that it evolved but by what mechanisms and (though
there is no answer to that), are these mechanisms a necessity of
a general universal biology?
Genetic Drift
Explores
Natural Selection
Fills Niches
Extinctions
Makes Room
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Evolution
Genetic Drift
Genetic drift implies that random statistical fluctuations are the
key driving forces of change and evolution.
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.
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Evolution
Natural Selection
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)
Natural selection as such does not imply that organisms need to
become more complex.
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Extinctions
Major types
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 of
groups 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
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Extinctions
Power of chance
Game with even-odds and an adsorbing boundary at zero. You
flip a coin H win, T lose.
Gambler’s stake
10
Number of plays
Similar results can be had in this
kind of scenario
When you reach the adsorbing boundary you are extinct in
money and cannot play again.
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Extinctions
Gambling for survival
A 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?
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Evolution
The Three Domains of Life on Earth
Archaea
Eucaryotes
Bacteria
Last common ancestor
Cells with primitive,
unregulated ATP synthetases
& protein synthesis
DNA genome
Protein synthesis
RNA world
Pre-biotic soup
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Genome size
Minimal Genome Size Needed for Life
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.
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Mycoplasma genitalium
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.
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Wrapping up
Key Points of the Day
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 ‘garbagebags’.
The origin of life is still far form clear!
Did life start here?
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Wrapping up
Give it some thought
Where did life originate?
References
Dive and Discover
The Cell, Alberts et al
Origin of Life, Freeman Dyson
The Origins of Life, John Maynard-Smith and Eors Szathmary
Kasting, J.F., 1993: Earth's early atmosphere. Science, v. 259, p. 920-926.
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