LIFE ON EARTH
Ref. Colby




A Brief History of Life

   Biologists studying evolution do a variety of things: population geneticists study
the process as it is occurring; systematists  seek to determine relationships between
species and paleontologists seek to uncover details of the unfolding of life in the
past. Discerning these details is often difficult, but hypotheses can be made and
tested as new evidence comes to light. This section should be viewed as the best
hypothesis scientists have as to the history of the planet. The material here ranges
from some issues that are fairly certain to some topics that are nothing more than
informed speculation. For some points there are opposing hypotheses -- I have tried to
compile a consensus picture. In general, the more remote the time, the more likely the
story is incomplete or in error. 
  
Abiogenesis is not evolution.  It is an attempt to explain the origin of life.  Many of
the hypotheses have been tested and found valid.  One may then extrapolate to explain
how life began, but obviously no one can return to the dawn of time.  Life started in
the sea.   It stayed there for the majority of the history of earth. 

   The first replicating molecules were most likely RNA. RNA is a nucleic acid similar
to DNA. In laboratory studies it has been shown that some RNA sequences have catalytic
capabilities. Most importantly, certain RNA sequences act as  polymerases -- enzymes
that form strands of RNA from its monomers. This process of self replication is the
crucial step in the formation of life. This is called the RNA world hypothesis. 
   The common ancestor of all life probably used RNA as its genetic material. This
ancestor gave rise to three major lineages  of life. These are: the prokaryotes
("ordinary" bacteria), archaebacteria (thermophilic, methanogenic and halophilic
bacteria) and eukaryotes. Eukaryotes include protists (single celled organisms like
amoebas and diatoms and a few  multicellular forms such as kelp), fungi (including
mushrooms and yeast), plants and animals. Eukaryotes and archaebacteria  are the two
most closely related of the three. The process of translation (making protein from the
instructions on a messenger RNA template) is similar in these lineages, but the
organization of the genome and transcription (making messenger RNA from a DNA template)
is very different in prokaryotes than in eukaryotes and archaebacteria. Scientists
interpret this to mean that the common ancestor was RNA based; it gave rise to two
lineages that independently formed a DNA genome and hence independently evolved
mechanisms to transcribe DNA into RNA. 

   The first cells must have been anaerobic because there was no oxygen in the
atmosphere. In addition, they were probably  thermophilic ("heat-loving") and
fermentative. Rocks as old as 3.5 billion years old have yielded prokaryotic fossils.
Specifically, some rocks from Australia called the Warrawoona series give evidence of
bacterial communities organized  into structures called stromatolites. Fossils like
these have subsequently been found all over the world. These mats of  bacteria still
form today in a few locales (for example, Shark Bay Australia). Bacteria are the only
life forms found in the  rocks for a long, long time --eukaryotes (protists) appear
about 1.5 billion years ago and fungi-like things appear about  900 million years ago
(0.9 billion years ago). 
  
   Photosynthesis evolved around 3.4 billion years ago. Photosynthesis is a process
that allows organisms to harness sunlight  to manufacture sugar from simpler
precursors. The first photosystem to evolve, PSI, uses light to convert carbon dioxide
(CO2) and hydrogen sulfide (H2S) to glucose. This process releases sulfur as a waste
product. About a billion years later,  a second photosystem (PS) evolved, probably from
a duplication of the first photosystem. Organisms with PSII use both  photosystems in
conjunction to convert carbon dioxide (CO2) and water (H2O) into glucose. This process
releases  oxygen as a waste product. Anoxygenic (or H2S) photosynthesis, using PSI, is
seen in living purple and green bacteria.   Oxygenic (or H2O) photosynthesis, using PSI
and PSII, takes place in cyanobacteria. Cyanobacteria are closely related to   and
hence probably evolved from purple bacterial ancestors. Green bacteria are an outgroup.
Since oxygenic bacteria are   a lineage within a cluster of anoxygenic lineages,
scientists infer that PSI evolved first. This also corroborates with  geological
evidence. 
   Green plants and algae also use both photosystems. In these organisms,
photosynthesis occurs in organelles (membrane   bound structures within the cell)
called chloroplasts. These organelles originated as free living bacteria related to the
cyanobacteria that were engulfed by ur-eukaryotes and eventually entered into an
endosymbiotic relationship. This  endosymbiotic theory of eukaryotic organelles was
championed by Lynn Margulis. Originally controversial, this theory is  now accepted.
One key line of evidence in support of this idea came when the DNA inside chloroplasts
was sequenced --  the gene sequences were more similar to free-living cyanobacteria
sequences than to sequences from the plants the chloroplasts resided in. 
   After the advent of photosystem II, oxygen levels increased. Dissolved oxygen in the
oceans increased as well as
atmospheric oxygen. This is sometimes called the oxygen holocaust. Oxygen is a very
good electron acceptor and can be  very damaging to living organisms. Many bacteria are
anaerobic and die almost immediately in the presence of oxygen.   Other organisms, like
animals, have special ways to avoid cellular damage due to this element (and in fact
require it to live.)   Initially, when oxygen began building up in the environment, it
was neutralized by materials already present. Iron, which   existed in high
concentrations in the sea was oxidized and precipitated. Evidence of this can be seen
in banded iron formations from this time, layers of iron deposited on the sea floor. As
one geologist put it, "the world rusted." Eventually, it grew to high enough
concentrations to be dangerous to living things. In response, many species went
extinct, some continued (and still continue) to thrive in anaerobic microenvironments
and several lineages independently evolved oxygen  respiration. 
   The purple bacteria evolved oxygen respiration by reversing the flow of molecules
through their carbon fixing pathways and modifying their electron transport chains.
Purple bacteria also enabled the eukaryotic lineage to become aerobic.  Eukaryotic
cells have membrane bound organelles called mitochondria that take care of respiration
for the cell. These are  endosymbionts like chloroplasts. Mitochondria formed this
symbiotic relationship very early in eukaryotic history, all but a few groups of
eukaryotic cells have mitochondria. Later, a few lineages picked up chloroplasts.
Chloroplasts have multiple  origins. Red algae picked up ur-chloroplasts from the
cyanobacterial lineage. Green algae, the group plants evolved from, picked up different
urchloroplasts from a prochlorophyte, a lineage closely related to cyanobacteria. 

   Animals start appearing prior to the Cambrian, about 600 million years ago. The
first animals dating from just before the  Cambrian were found in rocks near Adelaide,
Australia. They are called the Ediacarian fauna and have subsequently been  found in
other locales as well. It is unclear if these forms have any surviving descendants.
Some look a bit like Cnidarians   (jellyfish, sea anemones and the like); others
resemble annelids (earthworms). All the phyla (the second highest taxonomic  category)
of animals appeared around the Cambrian. The Cambrian 'explosion' may have been a
result of higher oxygen concentrations enabling larger organisms with higher
metabolisms to evolve. Or it might be due to the spreading of shallow seas at that time
providing a variety of new niches. In any case, the radiation produced a wide variety
of animals. 
   Some paleontologists think more animal phyla were present then than now. The animals
of the Burgess shale are an example of Cambrian animal fossils. These fossils, from
Canada, show a bizarre array of creatures, some which appear to have unique body plans
unlike those seen in any living animals. 
   The extent of the Cambrian explosion is often overstated. Although quick, the
Cambrian explosion is not instantaneous in geologic time. Also, there is evidence of
animal life prior to the Cambrian. In addition, although all the phyla of animals came
into being, these were not the modern forms we see today. Our own phylum (which we
share with other mammals, reptiles, birds, amphibians and fish) was represented by a
small, sliver-like thing called Pikaia. Plants were not yet present.   Photosynthetic
protists and algae were the bottom of the food chain. Following the Cambrian, the
number of marine families leveled off at a little less than 200. 
   The Ordovician explosion, around 500 million years ago, followed. This 'explosion',
larger than the Cambrian, introduced numerous families of the Paleozoic fauna
(including crinoids, articulate brachiopods, cephalopods and corals). The Cambrian
fauna, (trilobites, inarticulate brachiopods, etc.) declined slowly during this time.
By the end of the Ordovician, the Cambrian fauna had mostly given way to the Paleozoic
fauna and the number of marine families was just over 400. It  stayed at this level
until the end of the Permian period. 

   Plants evolved from ancient green algae over 400 million years ago. Both groups use
chlorophyll a and b as photosynthetic   pigments. In addition, plants and green algae
are the only groups to store starch in their chloroplasts. Plants and fungi (in
symbiosis) invaded the land about 400 million years ago. The first plants were
moss-like and required moist environments to survive. Later, evolutionary developments
such as a waxy cuticle allowed some plants to exploit more inland  environments. Still
mosses lack true vascular tissue to transport fluids and nutrients. This limits their
size since these must  diffuse through the plant. Vascular plants evolved from mosses.
The first vascular land plant known is Cooksonia, a spiky,  branching, leafless
structure.

   At the same time, or shortly thereafter, arthropods followed plants onto the land.
The first land  animals known are myriapods -- centipedes and millipedes. Insects
evolved from primitive segmented arthropods. The mouth parts of insects are modified
legs. Insects are closely   related to annelids. Insects dominate the fauna of the
world. Over half of all named species are insects.  One third of this number are
beetles. 
    Vertebrates moved onto the land by the Devonian period, about 380 million years
ago. Ichthyostega, an amphibian, is the  among the first known land vertebrates. It was
found in Greenland and was derived from lobe-finned fishes called  Rhipidistians.
Amphibians gave rise to reptiles. Reptiles had evolved scales to decrease water loss
and a shelled egg  permitting young to be hatched on land. Among the earliest well
preserved reptiles is Hylonomus, from rocks in Nova  Scotia. 
   The Permian extinction was the largest extinction in history. It happened about 250
million years ago. The last of the  Cambrian Fauna went extinct. The Paleozoic fauna
took a nose dive from about 300 families to about 50. It is estimated  that 96% of all
species (50% of all Families) met their end. Following this event, the Modern fauna,
which had been slowly  expanding since the Ordovician, took over. 

   The Modern fauna includes fish, bivalves, gastropods and crabs. These were barely
affected by the Permian extinction.  The Modern fauna subsequently increased to over
600 marine families at present. The Paleozoic fauna held steady at about  100 families.
A second extinction event shortly following the Permian kept animal diversity low for
awhile. 
   During the Carboniferous (the period just prior to the Permian) and in the Permian
the landscape was dominated by ferns  and their relatives. After the Permian
extinction, gymnosperms (ex. pines) became more abundant. Gymnosperms had  evolved
seeds, from seedless fern ancestors, which helped their ability to disperse.
Gymnosperms also evolved pollen, encased sperm which allowed for more outcrossing. 
   Dinosaurs evolved from archosaur reptiles, their closest living relatives are
crocodiles. One modification that may have been a key to their success was the
evolution of an upright stance. Amphibians and reptiles have a splayed stance and walk
with an undulating pattern because their limbs are modified from fins. Their gait is
modified from the swimming movement of  fish. Splay stanced animals cannot sustain
continued locomotion because they cannot breathe while they move; their undulating
movement compresses their chest cavity. Thus, they must stop every few steps and breath
before continuing on their way. Dinosaurs evolved an upright stance similar to the
upright stance mammals independently evolved. This allowed for continual locomotion. In
addition, dinosaurs evolved to be warm-blooded. Warmbloodedness allows an increase in
the  vigor of movements in erect organisms. Splay stanced organisms would probably not
benefit from warm- bloodedness.  Birds evolved from sauriscian dinosaurs.
Cladistically, birds are dinosaurs. The transitional fossils, Archaeopteryx and forms
from Asis,  have a mixture of reptilian and avian features. 

   Angiosperms evolved from gymnosperms, their closest relatives are Gnetae. Two key
adaptations allowed them to
displace gymnosperms as the dominant fauna -- fruits and flowers. Fruits (modified
plant ovaries) allow for animal-based   seed dispersal and deposition with plenty of
fertilizer. Flowers evolved to facilitate animal, especially insect, based pollen
dispersal. Petals are modified leaves. Angiosperms currently dominate the flora of the
world -- over three fourths of all living plants are angiosperms. 

   The end of the Cretaceous, about 65 million years ago, is marked by a minor mass
extinction. This extinction marked the demise of all the lineages of dinosaurs save the
birds. Up to this point mammals were confined to nocturnal, insectivorous niches. Once
the dinosaurs were out of the picture, they diversified. Morgonucudon , a contemporary
of dinosaurs, is an  example of one of the first mammals. Mammals evolved from
therapsid reptiles. The finback reptile Diametrodon is an  example of a therapsid. 

   The earth has been in a state of flux for 4 billion years. Across this time, the
abundance of different lineages varies wildly.   New lineages evolve and radiate out
across the face of the planet, pushing older lineages to extinction, or relictual
existence in protected refugia or suitable microhabitats. Organisms modify their
environments. This can be disastrous, as in the case of the oxygen holocaust. However,
environmental modification can be the impetus for further evolutionary change. Overall,
diversity has increased since the beginning of life. This increase is, however,
interrupted numerous times by mass  extinctions. Diversity appears to have hit an
all-time high just prior to the appearance of humans. As the human population  has
increased, biological diversity has decreased at an ever-increasing pace. The
correlation is probably causal.