Download Week 6

The origin and evolution of
life on Earth
Tuesday, October 8, 2013
How did life begin on Earth

Chapter 6

DNA & hereditary vs. spontaneity

Miller-Urey experiment
Tuesday, October 8, 2013
DNA & Hereditary

Last day, we discussed two out of three key features
of life on Earth
 structural units of life - cells
 metabolic processes that keep cells alive today

third feature
 reproduction of cells and the passing on of
hereditary information - DNA
Tuesday, October 8, 2013
The Structure of DNA

The “rungs” in the DNA
ladder are made of four DNA
bases (nucleotides)

Adenine (A)

Cytosine (C)

Guanine (G)

Thymine (T)

These are organic molecules
themselves

The backbone are phosphate
and sugar groups.

The sequence of these bases
encodes genetic information
Tuesday, October 8, 2013
Seeing is believing
A. Franklin & Gosling 1953 : X-ray diffraction photo 51 of B-DNA
B. Watson & Crick 1953 : model of the helical-X and layer lines in blue. (1962)
Tuesday, October 8, 2013
Replication of DNA
Other bases are floating in the cell
(recall that cells need liquid water)
Tuesday, October 8, 2013
How evolution works
Tuesday, October 8, 2013
How evolution works

In general, there are not enough resources (e.g. food) for
all organisms to survive and thrive.
Tuesday, October 8, 2013
How evolution works

In general, there are not enough resources (e.g. food) for
all organisms to survive and thrive.

Within a given population, individuals display variations in
their physical characteristics.
Tuesday, October 8, 2013
How evolution works

In general, there are not enough resources (e.g. food) for
all organisms to survive and thrive.

Within a given population, individuals display variations in
their physical characteristics.

Some traits will increase chances of survival and
subsequent reproduction, while others may decrease them
or make no difference.
Tuesday, October 8, 2013
How evolution works

In general, there are not enough resources (e.g. food) for
all organisms to survive and thrive.

Within a given population, individuals display variations in
their physical characteristics.

Some traits will increase chances of survival and
subsequent reproduction, while others may decrease them
or make no difference.

When traits are related to genetics (sequences of DNA),
then “successful” or naturally selected characteristics can
be preferentially passed on to the next generation.
Tuesday, October 8, 2013
How evolution works

In general, there are not enough resources (e.g. food) for
all organisms to survive and thrive.

Within a given population, individuals display variations in
their physical characteristics.

Some traits will increase chances of survival and
subsequent reproduction, while others may decrease them
or make no difference.

When traits are related to genetics (sequences of DNA),
then “successful” or naturally selected characteristics can
be preferentially passed on to the next generation.

Genetic information carried in DNA is the means by which
characteristics are inherited from one generation to the
next. It is difficult to imagine life without heredity.
Tuesday, October 8, 2013
Mono lake (CA)
Tuesday, October 8, 2013
Arsenic-driven life in Mono lake? (2010)
Tuesday, October 8, 2013
Arsenic-driven life in Mono lake? (2010)

Bacteria that had rewritten its DNA, preferring arsenic to phosphates for DNA
backbone

Debunked in 2012

But, just to be clear: finding an organism that didn’t need phosphorus, that used
arsenic instead, would be one of the most significant scientific discoveries of all
time. It would mean that Mono Lake was home to a form of life biologically
distinct from all other known life on Earth. This would suggest that life got
started on our planet not once, but at least twice, that the origin of life on
Earth was not a freak accident requiring highly specialized circumstances, but a
relatively commonplace event. And that in turn would strengthen the argument
that life is likely to be present on other worlds as well.
Tuesday, October 8, 2013
How did life originate on Earth?


All life today on Earth is
descended from other life
We do not see any cases of life
arising spontaneously


all modern-day cells contain
DNA, which is too sophisticated
for life to have originated
recently
However, the early Earth would
have been more suitable for the
spontaneous emergence of life



lots of organic material
little oxygen in the atmosphere
less competitive environment
Tuesday, October 8, 2013
The Miller-Urey experiment

Urey proposed that reactions in the atmosphere of the
early Earth would produce simple organic chemicals, e.g.
methane, ammonia, water, hydrogen sulphide.

Miller then demonstrated that combining a gaseous mixture
of the above chemicals in a spark chamber would create 22
types amino acids - some of the simplest building blocks of
life.

The Urey component of the experiment is still debated, i.e.
did the simple organics form in the atmosphere or via
volcanic outgassing. How long did the hydrogen last?

However, the Miller component has been extended to
demonstrate the creation of DNA-nucleotides and other
components of life.
Tuesday, October 8, 2013
Tuesday, October 8, 2013
Tuesday, October 8, 2013
CO2 → CO + [O] (atomic oxygen)
CH4 + 2[O] → CH2O + H2O
CO + NH3 → HCN + H2O
CH4 + NH3 → HCN + 3H2
These compounds then react under
high energy shock conditions,
forming amino acids (Strecker synthesis)
and other biomolecules:
CH2O + HCN + NH3 → NH2-CH2-CN + H2O
NH2-CH2-CN + 2H2O → NH3 + NH2-CH2COOH (glycine)
Tuesday, October 8, 2013
Miller-Urey today
Volcan Chaiten 2008
Tuesday, October 8, 2013
What causes lightening?
Scientists are still puzzled as to what triggers a spark during a thunderstorm.
The latest attempt to answer the question only adds to the intrigue.
by Philip Ball for BBC Future (27 Sept 2012)
It’s not yet agreed on how a thundercloud gets charged up in the first place. Somehow
the motions of air, cloud droplets, and precipitation (at that altitude, ice particles)
conspire to separate positive from negative charge at the scale of individual
molecules. It seems that ice particles acquire electrical charge as they collide, rather
as rubbing can induce static electricity, and that somehow smaller ice particles tend to
become positively charged while larger ones become negatively charged. As the
small particles are carried upwards by convection currents, the larger ones sink under
gravity, and so their opposite charges get separated, creating an electrical field.
A lightning strike discharges this field.
While many details of this process aren’t at all clear, one of the biggest mysteries is
how the spark gets triggered. Since the electrical fields measured in thunderclouds
don’t seem nearly big enough to induce a lightning discharge spontaneously,
something is needed to “seed” it. One idea is that they are triggered by cosmic rays
streaming into the atmosphere from space. [goes on to explain experiments]
Tuesday, October 8, 2013
Tuesday, October 8, 2013
The origin and evolution of
life on Earth
Tuesday, October 8, 2013
A Brief History of Life on Earth
Tuesday, October 8, 2013
A Brief History of Life on Earth

Biochemistry on Earth.

Miller-Urey experiment
Tuesday, October 8, 2013
A Brief History of Life on Earth

Biochemistry on Earth.


Miller-Urey experiment
RNA world & transition from chemistry to biology.

The first cell - the single common ancestor.
Tuesday, October 8, 2013
A Brief History of Life on Earth

Biochemistry on Earth.


RNA world & transition from chemistry to biology.


Miller-Urey experiment
The first cell - the single common ancestor.
Rise of life on Earth


basic code: 20 amino acids, DNA heredity, ATP-based cell energy.
The age of bacteria/archaea. The rise of eukareyea.
Tuesday, October 8, 2013
A Brief History of Life on Earth

Biochemistry on Earth.


RNA world & transition from chemistry to biology.


The first cell - the single common ancestor.
Rise of life on Earth



Miller-Urey experiment
basic code: 20 amino acids, DNA heredity, ATP-based cell energy.
The age of bacteria/archaea. The rise of eukareyea.
Where did this occur?



sides of deep sea volcanic vents (chemotrophs)
shallow ponds (phototrophs)
protected inside of rocks
Tuesday, October 8, 2013
Stromatolites 3.5 billion yr, photosynthesis.
Microfossils of ancient living cells?
Tuesday, October 8, 2013
Stromatolites 3.5 billion yr, photosynthesis.
Microfossils of ancient living cells?
Tuesday, October 8, 2013
Stromatolites 3.5 billion yr, photosynthesis.
Microfossils of ancient living cells?
Tuesday, October 8, 2013
A Brief History of Life on Earth
Tuesday, October 8, 2013
A Brief History of Life on Earth

Primitive anaerobic microbial life forms

anaerobic life doesn’t need molecular oxygen to survive
Tuesday, October 8, 2013
A Brief History of Life on Earth

Primitive anaerobic microbial life forms


anaerobic life doesn’t need molecular oxygen to survive
Rapid evolution and diversification due to high mutation rate
in RNA copying

fewer enzymes would have meant more RNA copying errors
Tuesday, October 8, 2013
A Brief History of Life on Earth

Primitive anaerobic microbial life forms


Rapid evolution and diversification due to high mutation rate
in RNA copying


anaerobic life doesn’t need molecular oxygen to survive
fewer enzymes would have meant more RNA copying errors
Photosynthesis and cyanobacteria => buildup of oxygen


extinction of many anaerobic microbes, rise of aerobic life forms
production of ozone, the land becomes habitable
Tuesday, October 8, 2013
A Brief History of Life on Earth

Primitive anaerobic microbial life forms


Rapid evolution and diversification due to high mutation rate
in RNA copying


fewer enzymes would have meant more RNA copying errors
Photosynthesis and cyanobacteria => buildup of oxygen



anaerobic life doesn’t need molecular oxygen to survive
extinction of many anaerobic microbes, rise of aerobic life forms
production of ozone, the land becomes habitable
Rise of multi-cellular organisms (about 1.2 Gyr ago)
Tuesday, October 8, 2013
A Brief History of Life on Earth

Primitive anaerobic microbial life forms


Rapid evolution and diversification due to high mutation rate
in RNA copying


anaerobic life doesn’t need molecular oxygen to survive
fewer enzymes would have meant more RNA copying errors
Photosynthesis and cyanobacteria => buildup of oxygen


extinction of many anaerobic microbes, rise of aerobic life forms
production of ozone, the land becomes habitable

Rise of multi-cellular organisms (about 1.2 Gyr ago)

The Cambrian Explosion (545 Myr ago)
Tuesday, October 8, 2013
A Brief History of Life on Earth

Primitive anaerobic microbial life forms


Rapid evolution and diversification due to high mutation rate
in RNA copying


anaerobic life doesn’t need molecular oxygen to survive
fewer enzymes would have meant more RNA copying errors
Photosynthesis and cyanobacteria => buildup of oxygen


extinction of many anaerobic microbes, rise of aerobic life forms
production of ozone, the land becomes habitable

Rise of multi-cellular organisms (about 1.2 Gyr ago)

The Cambrian Explosion (545 Myr ago)

Colonization of land (475 Myr ago)
Tuesday, October 8, 2013
RNA - transition from chemistry to biology?
Pre-cell (not living)
Tuesday, October 8, 2013
Cells (living)
RNA - transition from chemistry to biology?
Pre-cell (not living)
Tuesday, October 8, 2013
Cells (living)
The RNA world

“At some point a particularly remarkable molecule was
formed by accident. We will call it the Replicator. It
may not have been the biggest or the most complex
molecule around, but it had the extraordinary
property of being able to create copies of itself.”
Richard Dawkins

RNA is still a complex molecule.



How could such a molecule arise by chance?
Did increasingly complex cycles of organic chemical reactions
(perhaps facilitated by mineral clay surfaces) build the precursor of RNA?
Faster, more accurate replicators could then evolve
quickly and begin to dominate (DNA - fewer mistakes)
Tuesday, October 8, 2013
The RNA world
Natural selection gets started and can potentially lead to
longer RNA molecules storing more and more genetic information…
problem though are error rates!
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
U
C
G
U
C
G
C
T
U
G
U
T
G
G=C
U
G=C
G=C
C
G=C G
U
G=C
G=C C
G=A
G
C
G=C
G=C
T
G=C
U
G=C
G
G=C
G=C
U
G=C
G=C
G
T
G=C
G=C
Problem is that 1 in 20 nucleotides spontaneously mispairs in solutions…
- information can only be maintained if the error-rate is low.
- thus DNA outcompetes RNA for passing hereditary information, but RNA
still participates as ribozymes (protein enzymes acting as catalysts)
Tuesday, October 8, 2013
Could life have migrated to Earth after
originating elsewhere?
Tuesday, October 8, 2013
Could life have migrated to Earth after
originating elsewhere?

If life originated elsewhere in the Solar System, could it
have migrated to Earth on a meteorite or comet and seeded
life on Earth?

This idea is known as panspermia
Tuesday, October 8, 2013
Could life have migrated to Earth after
originating elsewhere?

If life originated elsewhere in the Solar System, could it
have migrated to Earth on a meteorite or comet and seeded
life on Earth?


This idea is known as panspermia
Challenges would include surviving the expulsion, potentially
millions of years in space, and the fiery descent to Earth.
Tuesday, October 8, 2013
Could life have migrated to Earth after
originating elsewhere?

If life originated elsewhere in the Solar System, could it
have migrated to Earth on a meteorite or comet and seeded
life on Earth?

This idea is known as panspermia

Challenges would include surviving the expulsion, potentially
millions of years in space, and the fiery descent to Earth.

Organic compounds such as amino acids can be transferred,
e.g., have been discovered within meteorites (Murchison).
Tuesday, October 8, 2013
Could life have migrated to Earth after
originating elsewhere?

If life originated elsewhere in the Solar System, could it
have migrated to Earth on a meteorite or comet and seeded
life on Earth?

This idea is known as panspermia

Challenges would include surviving the expulsion, potentially
millions of years in space, and the fiery descent to Earth.

Organic compounds such as amino acids can be transferred,
e.g., have been discovered within meteorites (Murchison).

But could this new life survive and grow on Earth.

and isn’t this just dodging the question?
Tuesday, October 8, 2013
Could life have migrated to Earth after
originating elsewhere?

If life originated elsewhere in the Solar System, could it
have migrated to Earth on a meteorite or comet and seeded
life on Earth?

This idea is known as panspermia

Challenges would include surviving the expulsion, potentially
millions of years in space, and the fiery descent to Earth.

Organic compounds such as amino acids can be transferred,
e.g., have been discovered within meteorites (Murchison).

But could this new life survive and grow on Earth.


and isn’t this just dodging the question?
or in reverse - Could life from Earth have seeded life
elsewhere in the Solar System?
Tuesday, October 8, 2013
Compound Class
Amino Acids
Concentration(ppm)
CM
CI
Aliphatic hydrocarbons
Aromatic hydrocarbons
Fullerenes
Carboxylic acids
Hydroxycarboxylic acids
Dicarboxylic acids &
Hydroxydicarboxylic acids
Purines & Pyrimidines
Basic N-heterocycles
Amines
Amides linear
cyclic
Alcohols
Aldehydes & Ketones
Sulphonic acids
Phosphonic acids
Tuesday, October 8, 2013
17-60
~5
>35
3.3
>1
> 300
15
14
1.3
7
8
> 70
>2
11
27
68
2
Abundances of soluble organic compounds in the
Murchison meteorite (Botta & Bada 2002, Sephton 2002, 2004)
Compound Class
Amino Acids
Concentration(ppm)
CM
CI
Aliphatic hydrocarbons
Aromatic hydrocarbons
Fullerenes
Carboxylic acids
Hydroxycarboxylic acids
Dicarboxylic acids &
Hydroxydicarboxylic acids
Purines & Pyrimidines
Basic N-heterocycles
Amines
Amides linear
cyclic
Alcohols
Aldehydes & Ketones
Sulphonic acids
Phosphonic acids
Tuesday, October 8, 2013
17-60
~5
>35
3.3
>1
> 300
15
14
1.3
7
8
> 70
>2
11
27
68
2
Martian microbes in ancient meteorite?
Beer (microbe rich rock sample) in space EuTEF on ISS housed samples until 2009
Tuesday, October 8, 2013
Those crazy Russians ... Phobos-Grunt (2009)
On the other hand - Galileo spacecraft sent into Jupiter
to avoid Earth contamination of the Jovian satellites.
Tuesday, October 8, 2013
Some Review Questions

Chapter 6, “Would you believe it?” p235

We discover an intact fossil of a eukaryotic cell that
seems to be 3.0 billion years old. Yes? No? Why?

We find evidence that suggests molecular oxygen was
abundant in Earth’s atmosphere when life arose.
Yes? No? Why?

We discover that the first life created in the lab has a
DNA genome, rather than a RNA genome. Yes? No? Why?
Tuesday, October 8, 2013
Summary: rise of life
Tuesday, October 8, 2013
Summary: rise of life

Volcanic outgassing (surface or deep sea) provides organic
chemical factory.
Tuesday, October 8, 2013
Summary: rise of life

Volcanic outgassing (surface or deep sea) provides organic
chemical factory.

Evidence points to life arising as early as was practically
possible (after the heavy bombardment phase).
Tuesday, October 8, 2013
Summary: rise of life

Volcanic outgassing (surface or deep sea) provides organic
chemical factory.

Evidence points to life arising as early as was practically
possible (after the heavy bombardment phase).

No evidence for a second genesis.
Tuesday, October 8, 2013
Summary: rise of life

Volcanic outgassing (surface or deep sea) provides organic
chemical factory.

Evidence points to life arising as early as was practically
possible (after the heavy bombardment phase).

No evidence for a second genesis.

Life has altered the composition of the Earth’s atmosphere.
Tuesday, October 8, 2013
Summary: rise of life

Volcanic outgassing (surface or deep sea) provides organic
chemical factory.

Evidence points to life arising as early as was practically
possible (after the heavy bombardment phase).

No evidence for a second genesis.

Life has altered the composition of the Earth’s atmosphere.

Without methanogens and photosynthesis Earth may have
been subject to a runaway greenhouse effect - similar to
Venus
Tuesday, October 8, 2013
Earth over time
stromalites
cyanobacteria
hydrogen & helium burned off31by solar wind.
Kasting et al 2004
Tuesday, October 8, 2013
Carbon isotope ratios in ancient rocks linked to
production of organic molecules?
• 13C isotope record back to 3.8 Gyr
• inorganic rock 13C:12C = 1:90
• higher % of 13C when 12C being used by organic molecules.
Tuesday, October 8, 2013
Stromatolites 3.5 billion yr, photosynthesis.
Microfossils of ancient living cells?
Tuesday, October 8, 2013
Stromatolites 3.5 billion yr, photosynthesis.
Microfossils of ancient living cells?
Tuesday, October 8, 2013
~500 Myr
Tuesday, October 8, 2013
The Cambrian Explosion

The Cambrian Explosion refers
to the rapid emergence of
diverse life-forms about 540
Myr ago

Four keys factors which may
have triggered this event:

rise in oxygen levels

increased genetic complexity

climate change (end of most
recent Snowball Earth
episode)

lack of predators
Tuesday, October 8, 2013
The KT impact
Tuesday, October 8, 2013

Several mass extinction events have been
observed in the fossil record since the
Cambrian explosion.

However, the KT event is also associated with
the Iridium layer - a thin band of iridium
rich deposits and ash.

Iridium is rare in the Earths crust, it should
sink to the Earth’s core with the iron during
differentiation. However, asteroids are rich in
iridium.

This led Luiz and Walter Alvarez (1978) to
propose that the KT event was triggered by
a massive impact (or series of impacts) by an
asteroid (>100 kg, >10 km).

The impact debris (ash, and dust) would have
spread throughout the atmosphere causing a
global cooling lasting years or decades.

The KT event marked the extinction of the
dinosaurs.
Tuesday, October 8, 2013
Craters in the Inner Solar System
Tuesday, October 8, 2013
Tunguska:
7.14am June 30th 1908
Tuesday, October 8, 2013
5 megaton asteroid airburst
20km
40km
Tuesday, October 8, 2013
5 megaton asteroid airburst
20km
40km
Tuesday, October 8, 2013
Are we safe now?
Comet Shoemaker-Levy 9 (July 1994)
Tuesday, October 8, 2013
The Likelihood and
Consequences of Impacts
Tunguska
SL9
KT Impact
Tuesday, October 8, 2013
How Much Warning Would We Have?
Comet Hyakutake (1997): 2 months
Comet Hale-Bopp (1997): 2 years
Comet McNaught (2007): 5 months
Comet Holmes (2007): 182 years
Tuesday, October 8, 2013
Tuesday, October 8, 2013
Tardigrades
Tuesday, October 8, 2013
(in
"E
cl.
ub
Cy
ac
an
ter
i
ac a"
ter
ia)
ob
Gr
Va
Str
(
rio
i
Ch
nc een
Fu
(e. am
A
u
l
oa
g
. so pl
pic ngi
., b en
an s pr
f
R
l
no
a
o
a
row p
d a ot
ed
Ar
m
g
o
&
n
e
m
i
t
e
l
n a les
ch
lga ists
s
a
l
p
a
a
l
ga
lga
tes
lex
lga
ae
e
e
e)
a
a
e)
>600 mya
>500 mya
>455 mya
>1.25 bya
>1.8 bya
>3.5 bya
LUCA: last universal
common ancestor
Tuesday, October 8, 2013
M
(m et
ul az
an ticel oa
im lul
als ar
)
>570 mya
Next days

Skim Ch 7

Try review questions Ch 6 
Questions #1-7, 11, 13, 15,-17, 33-39
Tuesday, October 8, 2013
Tuesday, October 8, 2013