BioInfo 4U

Steve's Quick Links

Steve's Home page

Steve's SGCEP Courses: Introductory Biology I and Biology II, and Environmental Science

Steve's VSU nonmajors introductory General Biology courses: I and II

Steve's VSU graduate level Molecular Phylogenetics course

Steve's FSU Introduction to Bioinformatics Laboratory course

Steve's FSU Comparative Genomics Outline

Steve's FSU GCG Workshops

Florida State University Department of Scientific Computing

High Performance Computing at Florida State University

Florida State University Biology Department

Guide to Online Higher Education in the United States


My View of Life

Steve Thompson

The famous evolutionist Theodosius Dobzhansky (1900-1975) provided a beautiful and insightful inscription on the inner cover of the classic textbook Evolution (1977) that reads: " Nothing in biology makes sense except in the light of evolution." These words ring true to me. Evolution provides the single, unifying, cohesive force that allows all of life to be explained. It is to the life sciences what the long sought holy grail of the unified field theory is to astrophysics.

What are your ideas and thoughts in this area, before I discuss mine?

  • Some Basics
  • Life on Earth -- the Big Picture
    • Major event timeline on Earth, and in more detail at Wikipedia.
    • Natural Selection and the idea of Contingency. All of life is in principle a guided 'mistake.'
    • Evolution is NOT progressive: improper but always used terms, e.g. higher vs. lower, primitive vs. advanced.
    • Stephen J. Gould and Wonderful Life.
    • "The history of life is not necessarily progressive; it is certainly not predictable. The earth's creatures have evolved through a series of contingent and fortuitous events." (Gould, 1994).
    • The Cambrian Explosion as seen in the Burgess Shale
    • Special places on the Earth allow us to 'see' this life.
      • The Burgess Shale occurs in Yoho National Park, British Columbia, just the other side of the Continental Divide from Banff, Canada.
      • The inner gorge and the rest of the Grand Canyon of the Colorado River in Arizona contains a huge swath of fossil history.

    • What are the MAJOR divisions of life on Earth?
      • A real old, but surprisingly insightful, albeit progressive, view of life as drawn by Haeckel in the late 1800's.
      • The old, but wrong view, and the Five Kingdom dogma: Bacteria, Protista, Fungi, Plants, and Animals, as proposed by Whittaker, (1969) and expounded on endlessly by textbooks and the popular press; e.g. Margulis and Schwartz (1998).
      • However, the actual Domains of life are Archaea, Bacteria, Eukaryota. Originally proposed by Woese, et al. (1990), this newer view of life is shown in The Big Tree of Life.
      • Also see the fantastic Web resource at the Tree of Life
      • But lateral gene transfer and primordial endosymbiosis considerably confounds the picture, e.g. as portrayed by W. Ford Doolittle (1999), and popularized by Lynn Margulis.
      • And here's a nice course summary Web Page of the Three Domain system of life. Note that microbial life is by far the hugest, in spite of the little circles usually drawn on these trees!
      • Norm Pace's Course at the University of Colorado, Boulder, describes the current status of life's classification, and the extreme diversity of microbial life on earth.

    • Some impressive statistics:

        We 'know' about 1.75 million species of life, but some people estimate that there are up to 100 million total species on the Earth, i.e. we don't even know most of life! Of these, only insects are estimated to have more species than the various microbial organisms - there are an estimated 5 X 10^30 microbial cells on Earth.

        About half of the Earth's organic carbon is in microbial life.

        Another way to think about this is microbial biomass is 10,000 times more than the total human biomass of the earth. And less than 1% of that life is able to be cultured in the laboratory.

        Just the top 150 meters of open ocean contain up to 1,000,000 cells per milliliter, about half are Archaea; ocean sediments contain about 1,000,000,000 cells per gram; topsoil contains about 10,000,000 cells in 5,000 distinct genomes per gram (numbers typical of Whitman, et al. 1998).

      • Craig Venter, the star bio-entrepeneur of human genome fame, completed a survey in 2004 of all the microbial life in the Sargasso Sea finding almost 1,500 different microbial species of which 150 had not yet been identified (2004).
      • And a 2005 article in Science highlighting the human gut states that almost 100 trillion individual organisms, around 10 times the number of human cells in your body, represented by almost a 1,000 different species, live in the human gastrointestinal tract. Our feces are about half microbes by weight (2005)!

    • Living in the Microbial World is a fantastic course designed by Lorraine Olendzenski for middle and high school teachers taught at the Marine Biological Laboratory in Woods Hole every summer, that investigates this diversity of microbial life on the earth, and teaches teachers how to show it to their students.
    • A 'real-life' example.
      • Elongation Factor 1 alpha -- a ubiquitous and essential protein, part of the ribosome, the organelle 'factory' where all proteins are 'manufactured' in all cellular life. And let's see it in "action."
      • You can align sequences of this protein or of the DNA that codes for it from a wide spectrum of life. The conservation is striking! The National Center for Biotechnology Information shows the gene in several alternative views.
      • Functional and structural sites align perfectly. The Genetics Computer Group's (GCG) Wisconsin Package SeqLab graphical user interface (GUI) was one of the major bioinformatics toolkits that I used in my work.
      • This conservation can be seen with a graph of the similarity across the dataset.
      • A phylogenetic tree made from these sequences agrees with The Big Tree.

    • Implications and discussion . . .

  • References
    • Backhed, F., Ley, R.E., Sonnenburg, J.L., Peterson, D.A., and Gordon, J.I. (2005) Host-bacterial mutualism in the human intestine. Science. 307, 1915-1920.
    • Dobzhansky, T., Ayala, F.J., Stebbins, G.L., and Valentine, J.W. (1977) Evolution. W.H. Freeman and Company, San Francisco, California, U.S.A. (The source of the original 1973 quote is obscure though it has been cited as being transcribed from the American Biology Teacher. 1973. 35, 125-129).
    • Doolittle, W.F. (1999) Phylogenetic classification and the universal tree. Science. 284, 2124-2129.
    • Gould, S.J. (1994) The evolution of life on the earth. Scientific American. 271, 84-91.
    • Margulis, L., and Schwartz, K.V. (1998) Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth. 3rd edition, W.H. Freeman and Company, New York, New York, U.S.A.
    • Whitman, W.B., Coleman, D.C., and Wiebe, W.J. (1998) Prokaryotes: The unseen majority. Proceedings of the Natlional Acadamy of Science, U.S.A. 95, 6578-6583.
    • Whittaker, R.H. (1969) New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms. Science. 163, 150-60.
    • Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.H., and Smith, H.O. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science. 304, 66-74.
    • Woese, C.R., Kandler, O., and Wheelis, M.L. (1990). Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the Natlional Acadamy of Science, U.S.A. 87, 4576-4579.
© 2013 Steven M. Thompson, acknowledgements and thanks to the Florida State University Biology Department for generously extending Web hosting and e-mail services beyond my FSU tenure.
fsu seal