From:    Chris Colby
To:      All                                    Msg #255, May-04-93 08:06PM
Subject: the history of life

Organization: animal -- coelomate -- deuterostome
From: colby@bu-bio.bu.edu (Chris Colby)
Message-ID: <118233@bu.edu>
Newsgroups: talk.origins


I posted a brief history of life a month (?) or so ago and asked
for criticisms(*). Here is a significantly expanded version. I plan
on adding this to my FAQ when I'm done. Ignore the writing style,
or lack of it, for now -- I'm just looking for pointers on content.
I'm out of my field (mostly) on this. Thanks - Chris

(*) thanks to all who responded
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A BRIEF HISTORY OF LIFE

Life evolved 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.

The common ancestor of all life probably used RNA as its genetic
material and was most likely a progenote -- an organism whose
genes were not  arranged into a genome. The progenote 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 multicelluar 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 progenote (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 long, long time -- fungi-like things appear about 900 MYA
(0.9 Billion years ago).

Somewhere along the way, photosynthesis evolved. 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 CO2 and H2S to glucose. This process releases
sulfur as a waste product. Later a second photosystem (PSII)
evolved, probably from a duplication of the first photosystem.
Organisms with PSII use both photosystems in conjunction to convert
C02 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 is 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 PSI and PSII for photosynthesis. 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 very
controversial, this theory is now virtually universally 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.

The advent of photosystem II brought about a large change in the
atmosphere of earth -- 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.

One lineage to evolve oxygen respiration was the purple bacteria.
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 also
endosymbionts just 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. Red algae picked up ur-chloroplasts from the
cyanobacterial lineage. Green algae, the group plants evolved from,
picked up different ur-chloroplasts from a prochlorophyte, a lineage
closely related to cyanobacteria.

Prior to the Cambrian (~600 MYA), animals start appearing; 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 descendents. Some look a bit like
Cnidarians (jellyfish, sea anemones and the like).

The Cambrian 'explosion' produced a wide variety of animals.
Probably all the phyla (the second highest taxonomic category) of
animals appeared around the Cambrian. 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. Although
creationists are fond of pointing to the Cambrian explosion as
evidence of their views -- they ignore four things 1.) Evidence of life
(including animals) prior to the Cambrian 2.) Although quick, the
Cambrian explosion is not instantaneous in geologic time 3.) Although
all the phyla of animals came into being, these were _not_ the
modern, derived 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 _Pikia_. 4.) Plants
were not yet present. The Cambrian explosion  is not evidence of a
single creation event producing the current biota.

Following the Cambrian, the number of marine families leveled off at
a little less than 200. The Ordovician explosion (~500MYA) 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.

Somewhere in between these two points, plants and fungi (in
symbiosis) invaded the land (~400 MYA). The first plants were moss-
like and required moist environments to survive. Later, evolutionary
developments such as a waxy cuticle and a vascular system allowed
some plants (for example ferns) to exploit more inland environments.
The first vascular land plant known is _Cooksonia_, a spiky,
branching, leafless structure. At the same time, or shortly thereafter,
arthropods (myriapods -- centipedes and millipedes) followed plants
onto the land.

By the Devonian period (~380 MYA) vertebrates had moved onto the
land, _Ichthyostega_ is the among the first known land vertebrates,
an amphibian. It was found in Greenland and was derived from lobe-
finned fishes called Rhipidistians. Amphibians gave rise to reptiles,
animals with 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 is Nova Scotia.

The Permian extinction (~250MYA) was the largest extinction in
history. 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 in existence met their end. Some
estimate that as many as 50% of all families went extinct (you have
to kill of 100% of the species in a family before it goes extinct, hence
the difference between the two numbers.) Following this event, the
Modern fauna, which had been slowly expanding since the
Ordovician, took over. The Modern fauna (including fish, bivalves,
gastropods and crabs) was barely affected by the Permian extinction
and 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.

The flora as well as the fauna changed following the Permian. 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 much
more abundant. Gymnosperms had evolved seeds (which ferns lack)
which helped their ability to disperse. Gymnosperms also evolved
pollen, encased sperm which allowed for more outcrossing. In ferns,
sperm must swim from the male organs to the female organs

During the Jurassic (~200 MYA) and Cretaceous (~150MYA) periods
the dinosaurs ruled and flowering plants (angiosperms), together
with insects, diversified.

Dinosaurs evolved from reptiles. [What's the name of that recently
discovered, early dinosaur?] One modification may have been a key
factor in their success -- posture. Amphibians and reptiles have a
splayed stance and walk with an undulating pattern because their
limbs are modified from fins and their gait is modified from the
movement a fish makes when swimming. These 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) and this allowed for continual
locomotion. In addition, dinosaurs evolved to be warm-blooded.
Warm-bloodedness allows an increase in the vigor of movements in
erect organisms. Splay stanced organisms would probably not benefit
from warm-bloodedness.

Angiosperms evolved two key adaptations that allowed them to
displace gymnosperms as the dominant fauna -- fruits and flowers.
Fruits allow for animal based seed dispersal (and deposition with
plenty of fertilizer 8-). Flowers evolved to facilitate animal,
especially insect, based pollen dispersal. Angiosperms currently
dominate the flora of the world -- over three fourths of all living
plants are angiosperms.

Insects, who radiated a great deal along with Angiosperms, dominate the
fauna of the world. Over half of _all_ named species are insects. One
third of this number are beetles.

The end of the Cretaceous (~65 MYA) is marked by a minor mass
extinction that was the demise of all the lineages of dinosaurs save
the birds. Once the dinosaurs were out of the picture, mammals --
previously confined to nocturnal, insectivorous niches -- diversified.
_Morgonucudon_ , a contemporary of dinosaurs, is an example of one
of the first mammals.

The study of the history of life on this planet reveals a planet in flux.
The abundance of various lineages varies wildly across geologic time.
New lineages can evolve and radiate out across the face of the planet,
pushing older lineages to extinction, or relictual existences in
protected refugia and/or suitable microhabitats. 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 evolution of humans. It
has decreased at an ever-increasing pace since. The correlation is
probably causal.

Chris Colby   ---      email: colby@bu-bio.bu.edu     ---
"'My boy,' he said, 'you are descended from a long line of determined,
resourceful, microscopic tadpoles--champions every one.'"
      --Kurt Vonnegut from "Galapagos"