Evolution – Biology 4250
                                                                                                         Dr. Adams
Review Sheet 4.2 – Test 4

The Original Biomolecular Evolution
– the Organic from Abiotic?
            If we assume organics came from the Earth’s abiotic environment, then:
        1. There must be some way of making these organics (without living organisms).
        2. There must be a source of energy to build these larger molecules.
        3. These larger organics must be able to polymerize.
        4. These larger organics must be stabilized – they’d have to persist in a harsh environment.

            Two major alternative hypotheses exist on the source of original simple organics:
        1. Abiotic C, H, O & N components of early atmosphere combined somehow – debate rages
over the contents of the atmosphere and water early in Earth’s history.  After all, conditions were
extremely harsh, and it is unclear what the pressure, temperature and early atmospheric components
were like.
        2. Earth was "seeded" with organics from space; cometary dust, meteorites (still leaves the
question of where and how these organics formed). For example, the 1969 Murchison, Australia
meteorite contained several amino acids (glycine, alanine, valine, proline, etc.; pg. 651).  Since life
produces almost exclusively L-stereoisomers of A. A.'s, and the meteorite containedapprox. equal
amounts of L- and D-stereoisomers, then the source of the A. A.'s was unlikely biological.

        Experiments: Miller (1953, 1992); Fox 1972 – ammonia, methane, and H. Provide sparks
(lightning)/UV radiation – tremendous number of organics (A.A.’s, sugars, nucleotides). However,
better understanding of the geochemical processes suggest early atmosphere contained – CO2 and
N2, much less conducive to organics formation.
        Still, the Oparin-Haldane Model was formulated, and can at least be used as a null hypothesis
against which to test new findings. The model basically approaches the three questions (and four
statements listed above): 1. – biotic from abiotic; 2. – polymers assembled that can a) store information
and b) catalyze reactions; 3. – add membranes (and energy sources) to get a living organism (Fig. 17.12).
        1. Biotic from abiotic: So far, experiments have not produced large amounts of one stereoisomer
only of nucleotides or amino acids. Nor have large amounts of ribose (as opposed to other sugars) been
made. Nucleotides can attach at several places to ribose (and do so). And without a chemical energy
source, no polymerization takes place. Getting to specific, self-replicating RNA molecules (with
appropriate chirality) seems difficult to say the least – perhaps other self-replicating systems evolved first
(3rd paragraph, pg. 657) that in turn promoted development of RNA chains. Certainly, we don’t know
much (yet).
        2. Polymerization: in water, although monomers can easily be polymerized (with an energy source),
they also hydrolyze rapidly. Need some stability – how?  Ferris, et al, have demonstrated that the
aluminum-silicate clay mineral Montmorillonite slows hydrolyzing decay, and short polynucleotides have
been formed (and remained) on clay surfaces; with repeated application of more nucleotides, the clay
catalyzes the reaction and the polynucleotides can be made longer, now up to 50 nucleotides long. 
Ferris and others have similarly assembled polypeptides up to 55 A.A.’s long. So, certainly more
experimental support than for step one.  Interestingly, the oldest known exposed rocks on Earth (3.7
byo) already contain evidence of life.  Older rocks with evidence for life may be very difficult to find
due to erosive/tectonic/volcanic disruptions, and the conditions were unlikely conducive to life on the
planet much earlier than that.
        3. Life becomes cellular -- the ancestor of all extant organisms: it seems pretty clear that,
regardless of how many times life may have "started" on the planet, that eventually one main
interbreeding lineage may have become THE one – the ancestor of all living things on the planet. We
all use the same coding mechanism, the same A.A.’s, etc., and this machinery is housed in a membrane
– a cell.
        Many experiments, particularly by Fox, et al, have generated protein containing "membranes", 
with, characteristics of cells (pick up other molecules, "division", etc.). As you already know,
phospholipids thrown in water spontaneously organize into bilayers; these protein/phospholipid
membranes can fuse. Still, even if "taken up" by these "cells", how do DNA/RNA take control? Still
unanswered by anything experimental.

Who is/are the Common Ancestor(s)
        Direct fossil evidence of life begins between 3.2 and 3.5 bya, and appears to be similar to extant
cyanobacteria (photosynthetic); this is already too advanced to give us a view of the early common
ancestor(s) (cenancestor). Fossils can’t help us here.
        Phylogenetic reconstruction, however, can help out – we look for the synapomorphies to assemble
the Tree of Life. However, morphological characteristics of the primitive prokaryotes lacked enough
diversity to assemble the tree. DNA/RNA/ Protein sequencing techniques give us much more character
diversity – similar (but not identical sequences – why?) for the same gene. The more the differences, the
longer the lineages have been apart (straightforward) – a sort of "molecular clock". Of course, if you
want to do this for all life, you need a gene that codes for the same, and an essential, functioning molecule
in ALL living things – the gene for small subunit ribosomal RNA is such a molecule.
        The phylogeny intimated by this rRNA, which is counter to the five kingdom classification of life, is
shown in Fig. 17.18, 17.21, and 17.23-24 (but see fig. 17.22). Prokaryotes have two VERY distinctive
separate evolutionary lines, one including virtually all the commonly known types, the other represented
by "extremists", living in various harsh conditions (Archaea). Interestingly, these Archaea (formerly
Archaebacteria) are apparently more closely related to Eukaryotes than the "typical" Bacteria. Eukarya
are relative newcomers, with less than 10% of the variation seen in the rRNA small subunit gene.        
Interestingly, in analyzing some genes, some Archaea actually have what appear to be Bacterial
genes – why? Because they ARE bacterial, picked up by the organism from another. This can happen
with these prokaryotic forms (lateral gene transfer). As for the common ancestor, all evidence points
to a rather sophisticated, evolved organism, or SET of organisms, not unlike modern bacteria, sometime
as early as perhaps 4 to as recently as 2 bya.  It may very well be that extant life's history does NOT
originate with a single life form, but an interconnected set of roots to the tree, a community of interacting
species readily swapping genes (which, needless to say, makes for an interesting base to the phylogeny
-- see Fig. 17.26
        (Read pages 673 – 675 for date of oldest known eukaryotes and cyanobacteria [almost identifiable
to extant forms, and apparently largely unchanged for 2 by])

Hypotheses for the evolution of the "Tree of Life" -- the descent from the "common" ancestor
        1.  The Universal Gene-Exchange Pool -- three ancestors of todays domains emerged from the
            pool at different times, with later emergence of Archaea and Eucarya making them appear more
            more closely related.
        2.  The Ring of Life -- the first eukaryote arose by the fusion of an archaen and bacterium.  Less
            support for this hypothesis (though see discussion of mitochondria, below), as there are
            significant gaps in molecular development with this theory, and no cytoskeletal control in
            either makes it difficult to envision the necessary phagocytotic event
        3.  The Chronocyte -- an independent organism that developed a cytoskeleton and phagocytotic
            capabilities.  Eventually, a digestion-resistant archaen is eaten and becomes the "nucleus".
            Several holes in this theory as well, including lack of evidence for such a chronocyte.
        4.  The Three Viruses/Three Domains --  viruses, with RNA gene for reverse transcriptase, in
            turn generates host DNA from host RNA.  Host, with developed resistance, in turn has more
            stable DNA than RNA, and DNA becomes THE molecule.

Origin of Organelles

        Mitochondria, widespread but not universal in Eukarya, and chloroplasts, more restricted in their
distribution, are therefore not defining characteristics of the Eukarya. Where did they come from? Both
have their own DNA, and analysis puts chloroplasts rRNA small subunit gene with the cyanobacteria,
and that for mitochondria within the Bacteria as well. Lynn Margulis’ endosymbiosis theory is correct!!

Chapter 18:  The Cambrian Explosion and Beyond

The Nature of the Fossil Record:  Understand how organic remains fossilize, and that occasionally
    flesh can be preserved under very restricted conditions.  Understand, also, that, like any data set,
    fossils present a biased look at the history of life, for several reasons.  Different organisms/organs
    fossilize or don't (presenting a DISTINCT taxonomic bias in the fossil record), different conditions 
    at time of fossilization and after fossil formation, different access to fossils, etc.  See * below.

KNOW
the following:
Timeline – pages 692 & 693:
        Time (mya) for beginning and end:
Proterozoic – Precambrian times
Phanerozoic eon:
   Paleozoic – with Cambrian, Ordovician, Silurian, Devonian, Carboniferous (M & P), Permian
   Mesozoic – with Triassic, Jurassic, Cretaceous
   Cenozoic – with Paleocene, Eocene, Oligocene, Miocene, Pliocene, Quaternary

Know Laurasia, Gondwana, Pangaea, India colliding with Asia, beginning and end of rise of
        Appalachians, Alps/Himalayas rise, formation of landbridge between North and South America

Know coelomate/acoelomate, diploblast/triploblast, protostome/deuterostome

Know times for:
        Animals
            First shelled organisms
            First chordates and first vertebrates
                    First tetrapods (amphibians), reptiles, mammals, birds, placental mammals
                    First hominids, appearance of Homo (sapiens)
            First insects, and first winged insects
        Plants
            First land plants
            First vascular plants (ferns), first seed plants, first flowering plants            

You should also understand connections, such as why land animals came after land plants, and
why insect diversification really took off after evolution of flowering plants

*Understand what we know comes largely from fossils, which have some inherent biases
(geographical [require some minimal sedimentation at least], taxonomic [organisms with hard
parts preserved better], and temporal [older fossils less numerous]).
        Some famous fossil deposits:
            Ediacaran Hills in south Australia
            Burgess Shales in British Columbia
            Chengjiang deposits in Yunnan province, China

Was Cambrian Explosion really Explosive?
        Molecular clocks suggest derivation of some lineages older than fossils suggest (NOT a
surprise). Older fossil finds starting to confirm these older dates.
        Even so, there DOES appear to be a very rapid evolution of morphological traits, not only
in complexity (meaning more complex developmental program) but size as well.  Increasing
oxygen levels, more ecological interactions, etc. may have driven this evolution, but still there
would have had to have been some significant genetic variability available to ALLOW for this
evolution.

Macroevolutionary patterns -- know the following:
        Radiations (why, for instance, mammals radiated significantly after the K-T asteroid)
        "Stasis" and "zigzag" evolution
        Gradualism
        Punctuated Equilibrium (stasis [in morphology] followed by rapid diversification).
        Mass Extinctions: The "Big Five" – especially the K-T asteroid
        Background Extinction
        Human driven Extinction (see middle paragraph page 719)
________________________________

One last tidbit:
C values (page 576 and handout) -- total DNA per cell does NOT correlate with organisms
    perceived morphological complexity or phylogenetic position.