II. Earth approximately 4.6 B years old.  Began cooling, and torrential rains occurred.  Volcanoes spewed noxious gases into air.  Meteorites also may have brought organic compounds to earth (recent ones have been shown to have amino acids and sugar alcohols in them).

III. Early Atmosphere
    A. Probably composed of highly reduced compounds, with no free oxygen.  Table below compares today's atmosphere with what was thought to be present 4 B years ago.

                xiii. The Genetic Code
                        1. Must have evolved very early on, as all present-day life shares
                            essentially the same code - another aspect of the unity of life
                        2. All amino acids that are hydrophobic have uracil as the
                            second base in their codon
                        3. All charged amino acids have either adenine or guanine in the
                            middle codon position
                        4. Suggests life may have tried other codes, but this one was superior
                        5. A mutation in early RNA of uracil for thymine plus substitution of
                            deoxyribose for ribose may have been one of several events that
                            allowed double stranded DNA to form.
                        6. Why was DNA superior to RNA over time?  Double stranded DNA
                            may prevent errors from accumulating during replication.

            3. Photosynthesis - The Next Big Advance
                    i. about 3.6 B years ago (or BYA) first organisms may begun carrying
                        on photosynthesis
                    ii. Most primitive organisms probably didn't evolve oxygen or even split
                        water yet - probably did cyclic photophosphorylation, that is, they
                        made ATP but no oxygen.
                    iii. Chlorophyll not yet around - other pigments used to absorb light
                        energy.
                    iv. Present day anaerobic photosynthetic bacteria are descendants of
                        such creatures
                    v. Later, more complex bacteria evolved non-cyclic photophosphorylation,
                        and water was split to get electrons, and oxygen liberated.  Around
                        3.5 BYA.
                    vi. Over millions of years, oxygen began accumulating in atmosphere (but
                        only after oxidizing all that free iron (making rust so to speak).
                    vii. By 540 MYA, atmosphere was approaching present day concentrations
                        of oxygen of 21%.
                    viii. This forever changed the world - a stratospheric ozone layer formed
                        (about 12 miles up in atmosphere - shielded earth from lethal UV rays)
                    ix. Now atmosphere was more reactive - oxygen is a potent oxidizer.
                    x. Many organisms would be killed by the oxygen, so some found habitats
                        devoid of oxygen (anaerobic organisms - like Botulinum bacteria, that
                        cause botulism).
                    xi. Others took advantage of oxygen to become more active
                    xii. Endosymbiotic events took place - two prokaryotic organisms merged
                            but stayed together as working partners
                            a. mitochondria - derived from bacterial ancestors
                                1. have their own DNA - more similar to prokaryotic DNA than
                                    eukaryotic DNA
                                2. membranes - double membranes -outer one more similar to
                                    eykaryotic ones (suggests derived from absorbing ancestor);
                                    inner membrane is structurally more similar to prokaryotes
                            b. chloroplasts - derived from photosynthetic bacteria
                                1. Similar arguments about DNA and membranes as for
                                    mitochondria
                    xiii. So, when did "life" arise?  At what point would the first organisms
                        be called "alive"?  Difficult question to answer.  Most likely evolution
                        of life from non-life was a gradual question.  Maybe best answer is
                        a paraphrasing of the court ruling on what is pornography: "I can't
                        define it exactly, but I know it when I see it."

IV. Earliest Fossils
    A. Not sure when first cells evolved - hard to find rocks that old, and earliest cells
        would not have left very good fossils
    B. But bacteria-like organisms that are 3.8 BY old have been found in rocks in
        Australia.
    C. Thus, life evolved from non-life in less than 600 M years!!  That's fairly rapid in
        geologic terms - suggests evolution of life is easier than first thought.  That gives
        hope that it may have evolved on other planets, and that if we search long
        enough, we'll find it!  What would you think or do if we found life on another
        planet?
    D. First cells were prokaryotic, and heterotrophic (ingest their food).  Later
        photosynthesizing organisms were autotrophs (make their own food).
    E. As environmental resources were used up by organisms, competition would
            increase - this would favor evolution of more efficient organisms.  Organismal
            complexity would increase through natural selection.
    F. Some organisms would begin using other resources not able to be assimilated by
            more primitive organisms.  Would require evolution of new enzymes to
            metabolize these compounds.  End result: evolution of more and more complex
            biochemical pathways through time.  So much for Behe's arguments of
            irreducible complexity - Behe's theories are really arguments of too limited an
            imagination!!
    G. Interesting facts - all organisms do glycolysis - most primitive form of
            respiration.  Only more recently evolved organisms do Krebs cycle respiration.
    H. But if all world was heterotrophic, resources would eventually be exhausted.
    I. Autotrophs came along - first ones probably used H₂S for a source of electrons.
                      2 H₂S ------->>>> 4H+     +     2S      +      4 e-
    J. These organisms called chemo-autotrophs - no light needed.  Can be found at
            deep-sea vents today, where there is little or no light.  Other organisms may
            have used NH₃, NO₃ or even H₂ as sources of electrons.
    K. Eventually, photosynthetic autotrophs evolved - use sunlight to break water to get
            electrons.

V. Earliest Eukaryotes
    A. If we accept that endo-symbiosis was origin of eukaryotes, we have to ask, why
        was it an advantage over being prokaryotic?
    B. Perhaps, as oxygen built up in the atmosphere, eukaryotic organisms were better
        adapted at tolerating it, and, they may have evolved new biochemical pathways to
        cope with ever increasing oxygen levels.  This eventually gave rise to the Krebs
        cycle and the cytochromes for electron transport.
    C. These additional pathways added 36 more ATP that could be extracted from
        glucose, as opposed to just the 2 from glycolysis.
    D. Extra energetic gain allowed life to become more active, and eventually,
        multi-cellular.  The explosion of multi-cellular life then took off!
    E. In the Precambrian (before 590 MY ago) life was mostly unicellular.
    F. After this period, multi-cellular life abounded, in what is called the Precambrian
        Explosion.  The "Big-Bang" of Evolution as it is sometimes referred to.
    G. Plants invaded land about 450 MYA, followed by the animals.