My View of Life
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
be explained. It is to the life sciences what the long sought holy grail
unified field theory is to astrophysics.
What are your ideas and thoughts in this area, before I discuss
- 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
- Evolution is NOT progressive: improper but always used terms,
e.g. higher vs.
lower, primitive vs. advanced.
- Stephen J. Gould
- "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
- Special places on the Earth allow us to 'see' this
- The Burgess Shale occurs in
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
- What are the MAJOR divisions of life on Earth?
- A real old, but surprisingly insightful, albeit progressive,
view of life as drawn by
in the late 1800's.
- The old, but wrong view, and the Five Kingdom dogma: Bacteria,
Plants, and Animals, as proposed by Whittaker,
(1969) and expounded
on endlessly by textbooks and the popular press; e.g.
- 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
- 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
- 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
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
- 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
- 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
- You can align sequences of this protein or of the DNA that
codes for it from a wide spectrum of life. The
striking! The National Center for Biotechnology Information shows
the gene in several alternative
- 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 . . .
- Backhed, F., Ley, R.E., Sonnenburg, J.L., Peterson, D.A., and
Gordon, J.I. (2005)
Host-bacterial mutualism in the human intestine. Science.
- Dobzhansky, T., Ayala, F.J., Stebbins, G.L., and Valentine,
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,
- Doolittle, W.F. (1999) Phylogenetic classification and the
Science. 284, 2124-2129.
- Gould, S.J. (1994) The evolution of life on the earth.
- 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.
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.