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Geology and the Fossil Record

Much of what we know about life's origins has come from the fossil record, and the study of how the earth has changed over time.

The Fossil Record

Sedimentary rock forms as layers of minerals settle out of water. Dead organisms are buried in these sediments, so the oldest fossils are found in the oldest (which are often the deepest) sediments. But how do we tell the age of the fossils?

Relative Dating
Because more recent sediments cover older ones, the strata (layers) of sedimentary rock present a record of organisms that have existed through time.

Absolute Dating
Unlike relative dating, absolute dating of fossils involves establishing a discrete age (in years) to the fossils under study. This is generally done via radiometric dating in which the half life of a radioactive isotope is used to calculate how long the substances in the fossil have been decaying. Half life is the time it takes for 50% of the original radioactive sample to decay to its stable form. It is not affected by temperature, pressure, or other environmental variables. Hence, radiometric dating is a reliable way to gauge the age of fossils. Examples:

Biogeography

The continents did not always exist as they are today. They once were present as a single land mass called Pangaea. This split into northern (Laurasia) and southern (Gondwanaland) land masses that then underwent further fragmentation. This process is known as continental drift. You can see the physical manifestation of abutment of the continental plates in some areas, such as the San Andreas Fault.

Living organisms rode the continents as they broke up, and their previously contiguous populations underwent allopatric speciation.

Phylogenies are linked to continental drift, with those land masses that first broke away still having the most primitive organisms (not counting human introductions of exotic species).

An excellent overview of the study of plate tectonics is once again provided by the University of California at Berkeley Museum of Paleontology.

The Origin of Life

Tracking the history of fossils and the changing continents tells us something about how life has changed over time, but the big question still remains...

How did life originate? We can't go back and watch. But many have contributed pieces of the puzzle, which has yet to be completed.

  • In 1924, Russian biologist Aleksandr (Alexander) Oparin published a paper entitled The Origin of Life, in which he suggested that chemical reactions in the primitive oceans could have eventually "created" life. The work was never translated from Russian, it had little impact at the time.

  • In 1929, British biologist J.B.S. Haldane published similar ideas, but still, they were still essentially ignored.

  • In 1936 Oparin published his ideas--first described in his paper--as a book entitled The Origin of Life. This was translated into several languages (including English), was widely read...and the race was on!

    The Primordial Ooze

  • Earth was formed 4.5 - 5 billion years ago.
  • Earliest life on earth appeared between 3.5 - 4 billion years ago.

  • The oldest known fossils are stromatolites--sedimentary rock with striations very similar to those made even now by extant cyanobacteria.

    What was Primordial Earth like?

  • The early atmosphere was composed mostly of

  • Eventually, sufficient cooling allowed pockets of liquid water to persist, and over the millenia, the oceans were formed. Still, there was no oxygen in the atmosphere.

  • The only organisms were obligate anaerobes, whose only metabolic pathway was fermentation.

    The Origin of the Oxidizing Atmosphere: Chlorophyll a Appears

  • There was no oxygen in the Earth's atmosphere until photosynthetic organisms appeared.

    How did the first cells appear?

  • 1953 - Stanley Miller (then a graduate student) and Harold Urey (then his major professor) at the University of Chicago built an apparatus that simulated the conditions of the primordial oceans.

  • Analysis of the reaction solution yielded...
  • Analysis of gas portion yielded

    Altering proportions of gases gave similar results, as long as there was no free oxygen, which would oxidize everything. (Remember: there was no oxygen in the primordial atmosphere.)

    Later experiments with the apparatus yielded...

    Meanwhile, back in Russia, Oparin was working with another aspect of the origin of early life.

  • Recall how shaking oil and water together can create a tiny interface layer of bubbles! Other substances can do this, too.

  • Oparin mixed gelatin (a protein) and gum arabic (a polysaccharide) and stirred them with a motion mimicking that of the early seas.

  • The results: tiny, stable, globular structures. He called these coacervates.

  • Adding additional substances to the reaction mixture yields different results...

    A coacervate with working enzyme systems inside can be called a protobiont.

    A protobiont has some of the properties of life, depending on what was added to the mix, but not all. To be considered truly alive, a thing must have...

    Early Genetic Material

  • It is generally believed that RNA was the original genetic material

    However, comparatively stable DNA might have conferred a tremendous selective advantage over RNA. Almost all known living organisms use it as their permanent genetic blueprint.

    Of course, there are some who remain unconvinced.

    Origins of Life and Metabolism: Prokaryotes

    The term "prokaryote" is more descriptive than phylogenetic, as the lack of a characteristic (in this case, a membrane-bounded nucleus) isn't a very good basis for classification. What is the meaning of the word "prokaryote?"
    pro =
    karyon =

    What is the meaning of "eukaryote"?
    eu =
    karyon =

    PROKARYOTES... They're everywhere.

    Formerly, all prokaryotes were lumped into "Kingdom Monera."
    Now, they are classified into distinct lineages:

    Note that the phylogenetic tree shows "Domain Bacteria" as branching from the universal ancestor first, and sister taxa Archaea and Eukarya branching off "next".

    Remember that the entire tree can be swiveled at any node, and it would be just as correct to have Archaea and Eukarya at the left of the diagram.

    This might be less confusing to some, as the very first fossil organisms are nearly indistinguishable from archaebacteria.

    Both Archaea and Bacteria are considered to be "prokaryotic"--pre-nuclear. They lack membrane bounded organelles or nuclei, though many do have internal membrane systems.

  • Archaean-like prokaryotes were the first inhabitants of earth, and spent the first 2 billion years after their appearance alone on earth.

  • A huge diversity of Bacteria exists today

  • Bacteria are both primitive and highly successful.
    (Remember: primitive does not equal inferior)

  • The divergence of prokaryotic taxa happened so long ago that it may not be possible to determine true evolutionary relationships.

    Prokaryotic Structure and Function

  • Prokaryotes may be unicellular, aggregate or colonial.
  • Some of the more derived species may have colonies with a division of labor among cells (analogous to multicellularity in "higher" organisms).
  • Bacteria may be classified by their shape: ...but Bbacterial shape may not reflect phylogenetic relationships, as there may be convergence in shapes (e.g., spirilla & spirochetes), as well as a variety of shapes in closely related bacteria. But shape is useful for grouping and identifying on a gross level.

  • Bacteria range in size from 1-5 micrometers--much smaller than most eukaryotic cells (100-1000 micrometers).

  • Bacterial genome consists of a single, circular chromosome of double-stranded DNA. This can be very large, and is organized in the nucleoid region of the cell.

  • The average bacterium has about 1000 genes on this nucleoid c'some.

  • a plasmid is a small, circular piece of DNA, and it may contain only a few genes. This replicates autonomously, and is not considered part of the bacterium's own genome. However, it may confer phenotypic traits on the bacteria containing it.

  • Genes on plasmids may confer antibiotic resistance and other mutant characters on bacteria that have them. (For example, some bacterial species are not toxic unless they have a plasmid allowing them to manufacture specific toxins (e.g., Clostridium spp.)

  • Another diagnostic character is the nature of the cell wall, which is present in most bacteria. (Exception: mycoplasmas, all of which are intracellular parasites) Two major types of cell wall can be distinguished with Gram Staining.

    Bacterial Reproduction

    Bacteria may reproduce asexually:

    ...or sexually

    Bacterial cells can be grown in culture on appropriate nutrient media (usually agar with broth added). A bacterial colony on an agar plate is called a lawn, and various species have characteristic lawn phenotypes.

    This can be very useful in the study of bacterial genetics!

  • Some species can form environmentally resistant structures called endospores, which is little more than the chromosome surrounded by a thick wall. It's nearly impossible to kill an endospore, so pathogens that can form them are particularly pernicious!

  • Competition exists at even the microscopic level. Antibiotics are substances that inhibit the growth of prokaryotic cells. They are manufactured not only by plants and fungi, but also by some bacteria.

    Metabolic Diversity of Prokaryotes

    Three basic types of organisms re: oxygen tolerance/metabolism

    In the Krebs Cycle, the terminal electron acceptor can be

    Four Main Categories of Prokaryotic Energy Transduction

    How did it all begin?

  • Early hypotheses about the origin of bacterial metabolism suggested that the earliest cells used ATP from the "primordial soup".

  • Problem: it's not likely there was enough ATP out there to fuel those newly made cells. ATP is highly unstable, and won't remain in solution for long.

  • More plausible is the idea that CO2 was the first Carbon source, and that early cells had plasma-membrane anchored enzymes that could oxidize inorganic compounds to make the energy needed to drive synthesis of carbon compounds.

    Ecological Importance of Prokaryotes

  • Along with fungi, they are the biosphere's main decomposers.
  • Many are symbiotic

    The Importance of Nitrogen Metabolism

    Let's have a look at the Nitrogen Cycle

    And here are some of our pals who perform this marvel:


    Nitrogen-fixing bacteria in the roots of a leguminous plant

  • Nitrogen fixation - conversion of atmospheric nitrogen to nitrogen compounds (ammonia, nitrite or nitrate) that are usable by plants

  • Denitrification - nitrate-->nitrite-->ammonia-->N2

  • Nitrosomonas spp. - converts ammonia to nitrite

  • Pseudomonas spp. - converts nitrite or nitrate into N2 (denitrification)

    (Note: Pseudomonas (e.g., aeruginosa and cepacia) are often opportunistic pathogens. A pathogen is a disease-causing agent.
    Although Pseudomonas are very common in the environment, they usually do not cause disease. However, in an immunocompromised animal, they can proliferate, creating a very difficult-to-treat infection. Many strains are resistant to a wide variety of antibiotics.) Hence, they are opportunistic pathogens.

    Prokaryotes as Pathogens: Koch's Postulates

    Everyone knows that certain bacteria can cause disease in plants and animals. In order for a microorganism to be declared the cause of a particular disease, however, it must meet the following criteria (Koch's Postulates): Some pathogens don't meet the postulates, so clinicians must be a little bit flexible when trying to determine how to treat difficult-to-culture pathogens.

    How do bacteria cause diseases?