Supplemental Lecture (97/03/31 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Brief Introduction to Biology
    1. A list of vocabulary words is found toward the end of this document
    2. "Nothing in biology makes sense except in the light of evolution." - Theodosius Dobzhansky
    3. At its most essential, life reduces to the following:
      1. function follows structure.
      2. covalent bonds (and photons) harbor potential energy.
      3. potential energy may be harnessed to build complex stuctures (i.e., molecules and molecular complexes).
      4. some molecules and complexes can template their own synthesis.
      5. faster/better templators increase in number faster.
    4. In this lecture we will consider some aspects of the diversity and evolution of life on earth.
  2. Origin of life
    1. Favorable environment:
      1. Life evolved in an environment that was one heck of a lot more favorable to the evolution of life than is today's Earth's environment.
      2. Particularly:
        1. there was no molecular oxygen
        2. there was a lack of super-sophisticated competing organisms (bacteria for example)
        3. there presumably were sufficient resources (having both terrestrial and extraterrestrial sources
      3. Consequently, it didn't take all that much to prosper.
    2. Self-templating molecules:
      1. The key step was the chance occurrence (but perhaps inevitable under the right circumstances) of molecules that were able to template their own replication (e.g., prototype RNAs and DNAs).
      2. In addition, there was probably some reasonably abundant mineral catalyst to move the operation (replication) forward.
    3. "Sea" of resources:
      1. To these molecules the environment represented a "sea" of resources free for exploitation.
      2. Naturally, those "self-replicating" molecules that were a little better at replicating and exploiting resources got the upper hand, especially as resources became limiting.
    4. Membrane enclosure/protocell:
      1. The next big steps were the development of methods of more active exploitation of the environment (e.g., enzymes or their equivalent) and finally a means of inhibiting competing replicators from co-opting exploitation mechanisms, i.e., the concept of the individual was invented.
      2. The latter was probably achieved by placing a semipermeable physical barrier between a replicator and the outside world. Voilà! a protocell is born.
    5. Keep in mind:
      1. The important things to keep in mind with all this origin of life stuff are:
        1. there was lots of time
        2. resources were present and, due to a lack of molecular oxygen, more stable than they would be today
        3. organisms have to be super-sophisticated only if competing against super-sophisticated organisms (or, in the land of the blind, the one eyed organism is queen)
  3. Early life
    1. Most fossil evidence for early life has been lost as a consequence of geological processes.
    2. The earliest undisputed fossils are of bacteria and date to 3.5 billion years before the present. Other evidence of early life, more controversial, argues for a date of the earliest life existing at least 3.8 billion years ago.
    3. Stephen Jay Gould:
      1. "Life on earth evolved quickly and is as old as it could be. . . For reasons related to the chemistry of life's origins and the physics of self-organization, the first living things arose at the lower limit of life's conceivable preservable complexity. Call this lower limit the 'left wall' for an architecture of complexity. Since so little space exists between the left wall and life's initial bacterial mode in the fossil record, only one direction for future increment exists---toward greater complexity at the right (which is not to say that once complexity is achieved, evolution to less complexity cannot or does not occur). Thus, every once in a while, a more complex creature evolves and extends the range of life's diversity in the only available direction. In technical terms, the distribution of complexity becomes more stronly right skewed through these occasional additions. But the additions are rare and episodic. They do not even constitute an evolutionary series but form a motley sequence of distantly related taxa, usually depicted as eukaryotic cell, jellyfish, trilobite, nautiloid, euryperid (a large relative of horseshoe crabs), fish, an amphibian such as Eryops, a dinosaur, a mammal and a human being. This sequence cannot be construed as the major thrust or trend of life's history. Think rather of an occasional creature tumbling into the empty right region of complexity space. Throughout this entire time, the bacterial mode has grown in height and remained constant in position. Bacteria represent the great success story of life's pathway. They occupy a wider domain of environments and span a broader range of biochemistries than any other group. They are adaptable, indestructible and astoundingly diverse. We cannot even imagine how anthropogenic intervention might threaten their extinction, although we worry about our impact on nearly every other form of life. The number of Escherichia coli cells in the gut of each human exceeds the number of humans that has ever lived on this planet. . . This is the 'age of bacteria'---as it was in the beginning, is now and ever shall be." (Gould, 1994)
  4. Age of bacteria
    1. The earliest organisms which one may unambiguously describe as life were simple cellular creatures we in all likelihood would classify as bacteria were they alive today. Bacteria are morphologically simple, for the most part tiny cells whose forte is the invention of biochemical pathways and consequent utilization of novel nutrient substances.
    2. Key biochemical innovators:
      1. All of the primary metabolic pathways were invented by bacteria. For example:
        1. glycolysis
        2. cellular respiration
        3. photosynthesis
    3. In fact, all cellular respiration (i.e., oxygen utilization) and photosynthesis (gathering of energy from the sun) is still done only by bacteria, much in the guise of the endosymbiotic (or eucaryotic cells) mitochondria and chloroplasts.
    4. In ecological terms, bacteria serve as the sole primary producers on our planet.
    5. Extreme environments:
      1. Various bacteria can live in the absence of oxygen, in the presence of high temperatures (100 degree C water, for example), and in extremely concentrated salt solutions.
      2. Many other types of bacteria, of course, can get along just fine in non-extreme environments, and are abundant just about everywhere.
      3. Wherever there is life on our planet, there are bacteria.
    6. The significance of bacteria is serving as no less than the original as well as current biochemically dominant organisms.
    7. In addition, bacteria serve as the probable ancestors to all extant organisms, bacteria or not bacteria.
    8. Harberors of genetic diversity:
      1. Finally, a significant fraction, perhaps a majority of the genetic diversity among living organisms is found among bacteria.
      2. "To most people, biodiversity means plants, animals, or maybe insects. These are the organisms that taxonomists' tallies put at the top of the numbers game, with more than 248,000 described species of plants, 750,000 species of insects, and 280,000 species of other animals. But these counts are less a reflection of the true biological richness of life on Earth than of our ability to count what we can see, such as differences in the shapes of leaves and fins, and the colors of feathers." (p. 1750, Service, 1997)
  5. Multicellular eucaryotes
    1. Plants and animals are colonies of cells:
      1. The one area in which bacteria are bettered is in the exploitation of a colonial existence. This is achieved, for example, by the multicellular eucaryotes: Plants and animals.
      2. Though even here, what allows these non-bacteria (eucaryotes) to so successfully exploit their multicellular niches is an almost complete reliance on endosymbiotic bacteria as sources of much of their chemical energy.
    2. Origin of animals:
      1. Animals likely made their appearance on earth (only) somewhere between 700 to 1200 million (1.2 billion) years ago, as compared with appearance of bacteria more than 3.5 billion (3500 million) years ago (the uncertainty comes from the poor fossil preservation of animals prior to their development of hard body parts).
      2. They were originally not terribly sophisticated things, though that changed with time, competition, and perhaps also significant changes in the abiotic environment.
    3. Water vertebrates:
      1. One lineage of animals evolved backbones and we call these vertebrates.
      2. Highly adapted water vertebrates (fish) were followed (in time) by water-land interface adapted vertebrates (amphibians) who represented an evolutionary response to the evolution of terrestrial green algae (plants).
    4. Land vertebrates:
      1. Plants that were better adapted to drier terrestrial conditions were followed into these climates by vertebrates which were better adapted to drier terrestrial conditions (the reptiles).
      2. Reptiles were highly successful and evolved a number of lineages, some of which we continue to describe as reptiles but others which we give new names to (e.g., the for the most part terrestrial vertebrates include mammals, birds, and the extinct dinosaurs).
      3. Another highly successful terrestrial animal lineage (non-vertebrate) is the insects. There are a number of other, and still many more lineages if other non-vertebrate and aquatic lineages are considered.
    5. Primates:
      1. Among mammals, there developed large brained, diurnal, grasping, arboreal animals with binocular vision (primates).
      2. One primate lineage specialized further, evolving large bodies and even larger (relative to body size) brains (apes).
    6. Obligate tool users:
      1. One ape lineage specialized as bipedal walkers (the hominids).
      2. In this lineage there evolved obligate tool use, language, and even larger brains (Homo).
  6. Humans are special?
    1. Culture is special:
      1. We, as humans, like to consider human animals to represent some sort of ultimate expression of something (e.g., evolution). In fact, in terms of the history of earth, we're not terribly special, except in terms of our expertise in the harnessing culture (for the good, the bad, and the evil).
      2. Of course, many other animals have culture (the non-genetic passage of information from generation to generation), but humans have, by far and away, exploited the cultural transmission (and modification) of knowledge more and better than any other organism, extant or extinct.
    2. Humans write the text books:
      1. However, since we are humans, and humans write the text books, you will find that humans are typically considered in otherwise unwarranted detail.
      2. This makes historical sense, certainly makes interesting reading, but is not sufficient reason to make oversize declarations of human importance.
  7. Universal tree
    1. Gauging evolutionary distance:
      1. Evolution has been very busy doing things other than bringing forth humanity, for better or for worse.
      2. Recently, we have come to describe the products of evolution in a very abstract manner, considering only certain measures of evolutionary distance which we consider to be correlates to evolutionary time (the time since lineage divergence). That is, evolution can today be considered (though not completely described) solely in terms of change in organism genotype (the order of bases in an organisms DNA) rather than, as it once was, solely in terms of organism phenotype (what an organism actually looks like).
    2. Mass genotypic comparisons can be summed up visually in something called a cladogram.
    3. Universal tree:
      1. Below is one such cladogram called the universal tree which represents the evolutionary relatedness of all cellular life such that distance of lines separating lineages (tips of branches) is a measure of evolutionary distance (i.e., time since divergence).
      2. The primary conclusions which one might make from observation of the universal tree are the following:
        1. In terms of genetic diversity, mankind makes only a minimal contribution.
        2. The majority of genetic diversity is found among unicellular organisms.
        3. Among eucaryotes, the majority of genetic diversity is found among protozoa.
        4. Among multicelled eucaryotes, genetic diversity is found among three lineages, plants, animals, and fungi.
        5. Among unicellular organisms, procaryotes (bacteria) dominate.
        6. All cellular life is thought to have evolved from a single universal ancestor.
  8. Illustration, universal tree

  9. Links
    1. Life (Molecular Biology for Beginners)
  10. Vocabulary
    1. Age of bacteria
    2. Early life
    3. Humans are special
    4. Multicellular eucaryotes
    5. Origin of life
    6. Universal tree
    7. Universal tree, illustration
  11. Practice questions
    1. Fossil evidence for the existence of life dating 3.5 billion or more years before present is rare. Yet, we do not take this as an indication that life on earth was necessarily rare at the time. Why might this be so? (hint: it is not a consequence of biological processes; short answer)[PEEK]
    2. The earliest undisputed fossils were of [PEEK]
      1. sea weed
      2. atoms
      3. bacteria
      4. primordial soup
      5. all of the above
      6. none of the above
    3. What type of organisms (i) probably served as the universal ancestor, (ii) are the biochemically dominant organisms on Earth today, and (iii) serve as the chemical energy generators within you and me? (short answer) [PEEK]
    4. In terms of their contribution to the genetic diversity of our planet, which group would you consider to be the most relevant? (circle best answer) [PEEK]
      1. obligate tool-using primates.
      2. animals with backbones.
      3. bacteria.
      4. single-celled organisms.
      5. all of the above (are equivalent).
      6. none of the above (makes a significant contribution to genetic diversity).
    5. Today, due to the power of molecular evolutionary techniques (e.g., the sequencing and comparison by computer of S23 rRNAs), it is now widely accepted that there are three major forms (a.k.a., domains) of cellular life: eubacteria, archaea, and the eucaryotes. Previously, based upon morphological classification alone, it was generally accepted that there were five major forms of life (called kingdoms). Four of these kingdoms made up what we now know makes up just a single domain. The final kingdom, however, is now known to have lumped two domains together. Which two domains do you think these are? [PEEK]
    6. Organisms with __________-type cells (i) probably did not serve as the universal cellular ancestor, (ii) are not the biochemically dominant organisms on Earth today, and (iii) do not serve as the chemical energy generators within you and me. However, they have exploited the many benefits of multicellualarity with impressive success. (short answer) [PEEK]
  12. Practice question answers
    1. fossil loss through geological processes
    2. iii, bacteria
    3. bacteria; procaryotes; half credit for mitochondria.
    4. iv, single-celled organisms. Bacteria are, of course, form a sub-set of single-celled organisms (and I'll give half credit for this answer).
    5. archaea and eubacteria
    6. eukaryote, eukaryotic, nucleus-containing.
  13. References
    1. Gould, S.J. (1994). The evolution of life on earth. Scientific American October:85-91.
    2. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 61-76.
    3. Service, R.F. (1997). Microbiologists explore life's rich, hidden kingdomes. Science 275:1740-1742.
    4. Vermeij, G.J. (1996). Animal origins. Science 274:525-526.
    5. Wienberg, S. (1994). Life in the universe. Scientific American October:43-49.