The Origin of Life Evolution

8/6/2019 The Origin of Life Evolution

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Frederick H. Willeboordse

[email protected]

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


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


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.


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/

The Origin of Life Evolution

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