SETI bioastro: Evolutionary Biology: On the Primeval Kingdoms

From: Larry Klaes (lklaes@bbn.com)
Date: Tue May 02 2000 - 15:11:36 PDT


Evolutionary Biology: On the Primeval Kingdoms
-------------------------------------------------

Recent evidence concerning horizontal gene transfer in primitive
organisms presents a challenge to the idea of a single universal
common ancestor for life on Earth. The three major domains of
life probably arose from a population of primitive cells
differing in their genes. (Includes related background material.)

EVOLUTIONARY BIOLOGY: ON THE PRIMEVAL KINGDOMS

During most of the past 100 years, the consensus view among
biologists was that all life on Earth evolved from a universal
common ancestor, a primitive cellular form that lived
approximately 3.5 to 3.8 billion years ago. This view capped
centuries of detailed classifications of living systems, with
relationships between organisms deduced and revised and revised
again as new discoveries were made. Detailed analysis of many
traits indicated, for example, that primates in the human family
(hominids) shared a common ancestor with apes, that this common
ancestor shared an earlier common ancestor with monkeys, and that
that common ancestor, in turn, shared an even earlier common
ancestor with primitive primates (prosimians; e.g., lemurs), and
so on. The view was thus of a "tree of life", with discrete
branches rising ever higher, but with all branches deriving from
a single primeval trunk. The known organisms that might have
comprised the primeval trunk and its lowest branches, however,
did not provide enough organismic information to define detailed
relationships, so that biologists were left with apparent
mysteries concerning radical evolutionary innovations between
primitive cells and more complex cells, between the first
biological cells and the appearance of multicellular fungi,
plants, and animals.

... ... W. Ford Doolittle (Dalhousie University, CA) presents a
review of recent changes in evolutionary theory concerning
primeval origins, the author making the following points:

     1) In the mid-1960s, Zuckerkandl and Pauling proposed a
revolutionary strategy that might supply the missing information
concerning evolutionary branching. The essential idea was that
instead of investigating anatomy and physiology, family trees of
living organisms should be based on differences in the monomer
sequences in selected genes or proteins. This approach became
known as "molecular phylogeny", and its essential basis was that
as a result of changes in genes caused by mutations, as two
species diverge from an ancestor, the gene sequences they share
will also diverge, and as time passes, the genetic divergence
will increase. Researchers could thus reconstruct the
evolutionary past of living species by assessing the apparent
history of divergence of genes or proteins isolated from those
species. Protein studies completed in the 1960s and 1970s
demonstrated the general utility of molecular phylogeny by
confirming and then extending the already established family
trees of well-studied groups such as the vertebrates.

     2) A new research development occurred in the late 1970s,
when Carl Woese proposed that the two-domain view of life that
divided living organisms into a) bacteria and b) cells with
internal membrane-bound organelles (eukaryotes) was no longer
tenable on the basis of molecular analysis. Woese suggested that
certain so-called "bacteria" formed a distinct third primary
group -- the archaea -- and that members of this group were as
different from other bacteria as bacteria were different from
eukaryotes. Woese suggested that although certain cells without
internal membrane-bound organelles (prokaryotes) classified as
bacteria might look like bacteria, they were genetically much
different, and their *ribosomal RNA (rRNA) supported an early
evolutionary divergence.

     3) Once the idea of three rather than two primeval domains
was accepted by researchers, an important question was which of
the two structurally primitive groups -- bacteria or archaea --
gave rise to the first eukaryotes? Because of evidence indicating
an apparent kinship between the gene expression/protein synthesis
machinery of archaea and eukaryotes, the consensus was that
eukaryotes diverged from the archaea.

     4) One important result of research in molecular phylogeny
during the past 15 years has been the production of strong
evidence supporting the "endosymbiont hypothesis". In biology,
the term "symbiosis" refers in general to an intimate and
protracted association of individuals of different species, and
"endosymbiosis" refers to a symbiotic association between cells
of two or more different species in which a smaller cell inhabits
a larger host cell. The endosymbiont hypothesis in evolutionary
biology, now a consensus view, proposes that the mitochondria
components of eukaryotes, so essential for eukaryote metabolism,
formed when an early eukaryote engulfed and then retained one or
more primitive bacteria of a certain type (alpha-proteobacteria).
Eventually, these bacteria relinquished their ability to live on
their own and transferred some of their genes to the nucleus of
the host cell, and these bacteria then evolved into the extant
mitochondria. In addition, and similarly, the hypothesis proposes
that some mitochondria-bearing eukaryotes ingested bacteria
capable of producing oxygen during photosynthesis
(cyanobacteria), and these resident symbiotic bacteria
subsequently evolved into the chloroplasts, the present internal
structures that drive photosynthesis in certain eukaryotes (e.g.,
in plant cells).

     5) Until very recently, therefore, the consensus view in
biology could be summarized as follows: The early descendants of
the last universal common ancestor -- a small prokaryote cell --
divided into two prokaryotic groups: the bacteria and the
archaea. Later, the archaea gave rise to the eukaryotes.
Subsequently, the eukaryotes gained valuable energy-generating
organelles -- mitochondria and (in the case of plants, for
example) chloroplasts -- by taking up and retaining certain
symbiotic bacteria.

     6) Several years ago, however, the consensus view stated
above became complicated by a large amount of evidence concerning
the phenomenon of "lateral gene transfer" (horizontal gene
transfer). Biologists recognize two types of gene transfer from
one organism to another: vertical and horizontal. Vertical gene
transfer occurs between parents and offspring, and horizontal
gene transfer is the transfer that may occur between organisms
otherwise. It is in bacteria that horizontal gene transfer has
been studied most extensively, particularly in the last decade.
Three types of horizontal gene transfer are known: conjugation,
transduction, and transformation. Conjugation is a type of sexual
reproduction exhibited by some bacteria, the process involving
the exchange of genetic material by means of a tube or bridge,
the transfer of DNA occurring either in one direction or in both
directions. Transduction involves the transfer of genetic
material from one bacterium to another with the intermediation of
a virus. Essentially, when the virus infects one bacterium, it
often carries away pieces of that bacterium's genome, and those
pieces, upon the infection of a new bacterium, become
incorporated into the second bacterial genome. Finally,
transformation is the process involving the uptake or
incorporation of DNA fragments (plasmids) by a bacterium, first
observed in 1944 by Oswald Avery. In this context, the important
aspect of horizontal gene transfer is that in primitive cells
such as prokaryotes it is now apparent that horizontal gene
transfer readily occurs across species. As a consequence of the
new evidence, the consensus view of the interrelations between
the primeval three kingdoms has now been seriously destabilized.

     7) In general, the current situation concerning the
evolutionary "tree of life" is as follows: The conceptual tree-
like structure with discrete branches is retained at the top of
the eukaryote domain, and also retained is the idea that
eukaryotes obtained mitochondria and chloroplasts from bacteria.
But the lower parts of the tree are now seen to involve an
extensive anastomosis of branches -- branches joining other
branches in a complex network of intersecting links -- resulting
from extensive horizontal gene transfer of single or multiple
genes, the horizontal gene transfer known to be common in
unicellular organisms. Thus, the author (Doolittle) suggests that
the "tree of life" lacks a single organism at its base, and that
"the three major domains of life probably arose from a population
of primitive cells that differed in their genes."

-----------
W. Ford Doolittle: Uprooting the tree of life.
(Scientific American February 2000)
QY: W. Ford Doolittle, Dalhousie Univ., Halifax, Nova Scotia, CA.

-----------
Text Notes:

... ... *ribosomal RNA (rRNA): A ribosome (not to be confused
with riboZYME) is a small particle, a complex of various
ribonucleic acid component subunits and proteins that functions
as the site of protein synthesis.

-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 5May00
For more information: http://scienceweek.com/swfr.htm

-------------------
Related Background:

ORIGIN OF LIFE: A MODEL FOR THE UNIVERSAL ANCESTOR

Biologists have long subscribed to the idea that all life on
Earth arose from a common ancestor. Until recently, nothing
concrete was said about this ancestor, but it was intuitively
assumed to be simple, often likened to a *prokaryote, and
generally held to have had little or no *intermediary metabolism.
Only when biology became defined on the level of molecular
sequences did it become possible to seriously consider the nature
of this ancestor. ... ... Carl Woese (University of Illinois
Urbana-Champaign, US) presents a "genetic annealing" model for
the universal ancestor of all extant life. Physical annealing
involves a first stage heating to a high temperature followed by
a slow cooling of the system to produce new structures,
particularly special crystalline forms. The term "annealing" is
also used in molecular biology to refer to the separation of DNA
strands by heating and the recombination of complimentary strands
by cooling. In Woese's model, the term "annealing" is used in
still a third sense. In the author's model, in the evolutionary
counterpart of physical annealing, the elements of the system are
primitive cells, mobile genetic elements, and so on, and physical
temperature becomes "evolutionary temperature", the evolutionary
"tempo". The evolutionary analog of "crystallization" is
emergence of new structures, new cellular subsystems that are
refractory to major evolutionary change. The author defines the
entities in which *translation had not yet developed to the point
that proteins of the modern type could arise as "progenotes", and
the era during which these were the most advanced forms as the
"progenote era". Concerning "evolutionary temperature", the
author points out that macroscopic evolutionists recognized long
ago a relationship between the "tempo" (rate) of evolution and
its "mode" (a measure of the outcomes). When microbial evolution
finally came into the picture, a similar phenomenon was
encountered on the molecular level, suggesting that this
tempo/mode relationship was a fundamental manifestation of the
evolutionary process. Because of high mutation rates and other
factors, the progenote era is proposed as one of very high
evolutionary tempo. In the author's model, progenotes were very
unlike modern cells, their component parts with different
ancestries, and the complexion of their components changing
drastically over time. Progenotes possessed the machinery for
gene expression and genome replication and at least some
rudimentary capacity for cell division, but the ordinary cellular
functions had no genealogical continuity, since they were too
subject to the confusion of *lateral gene transfer. According to
the author, the transition from progenotes to genotes turned upon
the evolution of translation, the conversion of messenger RNA
code into the specific amino acid sequences of specific proteins.
The author proposes the genetic annealing model as "an attempt to
develop a consistent general picture of the universal ancestor...
The ancestor cannot have been a particular organism, a single
organismal lineage. It was communal, a loosely knit, diverse
conglomeration of primitive cells that evolved as a unit... The
universal ancestor is not an entity, not a thing. It is a process
characteristic of a particular evolutionary stage." The author
concludes with a conjecture that genomes resulting from episodes
of rapid evolution will contain an abnormally high proportion of
foreign genes, and a suggestion that "genome sequences will soon
be available in sufficient number to properly test whether the
tempo/mode relationship (rapid evolution) invariably links
increased mutation rate and increased levels of lateral gene
transfer or vice versa."

QY: Carl Woese (carl@ninja.life.uiuc.edu)
(Proc. Natl. Acad. Sci. US 9 Jun 98 95:6854)
(Science-Week 3 Jul 98)

... ... *prokaryote: Prokaryotes are cells without a cell nucleus
and other membrane-bound organelles.

... ... *intermediate metabolism: The sum of all metabolic
reactions between the uptake of nutrients and the excretion of
waste products.

... ... *lateral gene transfer: See main report.

-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 3Jul98
For more information: http://scienceweek.com/swfr.htm

-------------------
Related Background:

BIO-TAXONOMY: EMERGENCE OF A SHARP PERSONAL CONTROVERSY

In a recent report (see Related Background material below) we
briefed a proposal by Ernst Mayr for a return to the *prokaryote-
eukaryote domain dichotomy from the present *archaea-eubacteria-
eukaryote domain trichotomy that has come to be used by many
biologists during the past decade. The details of the distinction
are provided in the report attached below, so we will not repeat
them. The controversy is of some interest in biology, as perhaps
a possible controversy concerning the present standard model
classification scheme of fundamental particles and forces in
physics would be to physicists. The domain trichotomy idea in
bio-taxonomy was first proposed in the 1980s by Carl Woese, who
like Ernst Mayr, is a member of the US National Academy of
Sciences. Writing in the same journal in which Mayr's proposal
appeared a few weeks ago, Woese now attempts to rebut Mayr's
ideas with an apparent singular vehemence, proposing that the
issue is more profound than that of merely assessing the utility
of a classification scheme. Woese writes: "If there were ever an
issue in biological classification that cannot be settled by
pedantry, it is this one." [Editor's note: This is not completely
gratuitous, since in his paper Mayr states, "Here it must be
remembered that Woese was not trained as a biologist and quite
naturally does not have an extensive familiarity with the
principles of classification."] And again from Woese: "To Mayr,
the issue is one of whether we should define two or three domains
and what the classificatory precedents or rules for deciding this
are. However, the *universal phylogenetic tree tells us that the
domains are unique among taxa and that their number and their
composition are not subject to classificatory fiat, but are
naturally defined." Woese's idea, apparently, is that the
trichotomous classification scheme is discovered rather than
constructed, which implies a significant problematic
philosophical subtext that is not amplified in his paper. In
summary, Woese makes the following points concerning his
position: 1) Mayr's article is not a taxonomic quibble but a "de
facto pronouncement on the nature of biology." A biological
classification is in effect an overarching evolutionary theory
that guides our thinking and experimentation, and it must be
structured to reflect evolutionary reality. 2) The prokaryote-
eukaryote dichotomy, which Mayr proposes to reinstitute, is a
failed taxonomic theory that was never recognized as theory and
therefore never tested in a timely fashion, with the consequence
that it has adversely affected the development of biology,
especially microbiology, in the latter half of this century. 3)
The scientifically perceived importance of a group of organisms
must reflect the natural importance of the group. 4) Microbial
diversity is far more than a listing of distinguishable microbial
species. We need to understand the quality of microbial
diversity, for it is the diversity that defines the biosphere of
this planet. 5) Evolution must be integrated into the fabric of
molecular biology... Any comprehensive understanding of a
biological entity, be it an organism or a molecule, necessarily
has an evolutionary component. Woese concludes: "The disagreement
between Dr. Mayr and myself is not actually about classification.
It concerns the nature of Biology itself. Dr. Mayr's biology
reflects the last billion years of evolution; mine, the first
three billion. His biology is centered on multicellular organisms
and their evolutions; mine on the *universal ancestor and its
immediate descendants. His is the biology of visual experience,
of direct observation. Mine cannot be directly seen or touched;
it is the biology of molecules, of genes and their inferred
histories. Evolution for Dr. Mayr is an "affair of phenotypes".
For me, evolution is primarily the evolutionary _process_, not
its outcomes. The science of biology is very different from these
two perspectives, and its future even more so." [Editor's note:
Ignoring the personalized undercurrents, the essential
controversy here is apparently between a classification system
based on utility criteria and observed similarities and
differences among entities (Mayr), and a classification scheme
based on theoretical and experimental molecular-genetic
relationships (Woese). The question of why there must be only one
classification scheme in use by working biologists is not
addressed by either Mayr or Woese.]

-----------
C.R. Woese (University of Illinois Urbana-Champaign)
Default taxonomy: Ernst Mayr's view of the microbial world.
(Proc. Natl. Acad. Sci. US 15 Sep 98 95:11043)
QY: Carl R. Woese <carl@ninja.life.uiuc.edu>

-----------
Text Notes:

... ... *prokaryote-eukaryote domain dichotomy: See report
attached below.

... ... *archaea-eubacteria-eukaryote domain trichotomy: See
reports attached below.

... ... *universal phylogenetic tree: Refers to the present
taxonomic-evolutionary classification scheme for all life on
Earth.

... ... *universal ancestor: Refers to the common ancestor from
which all life on Earth is considered to have derived.

-------------------
Summary & Notes by SCIENCE-WEEK <http://scienceweek.com> 16Oct98

-------------------
Related Background:

BIO-TAXONOMY: A PROPOSAL FOR ONLY TWO EMPIRES

The physicist confronting bio-taxonomy for the first time may
experience bewilderment: there are in excess of 30 million
species of life forms, the classification system is far from
simple, the system has some historically based confusions, and
the system is frequently redefined. Perhaps only the organic
chemist can feel a full empathy here, since organic chemistry is
faced with the similar problem of classifying millions of organic
chemical entities. A fundamental consideration is that in the
context of such a diversity of objects, a self-consistent
classification scheme is of extreme importance. At the present
time, in biology, there is a significant controversy concerning
primary categories, and that is the subject of this report. Two
main groups of life forms have been recognized for some time,
prokaryotes and eukaryotes. Prokaryotes are cells without a cell
nucleus and other membrane-bound organelles, and eukaryotes are
cells with a cell nucleus and other membrane-bound organelles.
(Organisms composed of eukaryote cells are also called
"eukaryotes"). For example, all bacteria are prokaryotes; all
complex animals, plants, etc., are eukaryotes. Fifteen years ago,
C.R. Woese (University of Illinois Urbana-Champaign, US) proposed
that the prokaryotes actually consist of two main groups, the
eubacteria and the archaebacteria, and that the differences
between these two groups are as great as the differences between
prokaryotes and eukaryotes, and that as a consequence a
tripartite primary scheme should be used, the primary categories
(kingdoms or empires) consisting of Eubacteria, Archaebacteria,
and Eukaryotes. Woese's differentiation of eubacteria and
archaebacteria was based on *habitats, cell wall constituents,
genome organization, and various aspects of protein synthesis
biochemical machinery, and during the past decade most biologists
have apparently accepted his categorization scheme. ... ... Now
Ernst Mayr (1904- ), a prominent biologist, proposes a rejection
of the Woese categorization and a return to a scheme involving
only 2 primary categories (empires), the Prokaryotes and
Eukaryotes. Mayr makes the following points: 1) A classification
scheme is essentially an information storage and retrieval
system, permitting the location of an entity with a minimum of
effort and loss of time, the objective optimally achieved by
arranging entities in a hierarchy of classes, ranked by degree of
similarity. 2) Evidence indicates that the archaebacteria are so
much more similar to the eubacteria than to the eukaryotes, that
their removal from the prokaryotes is not justified. The
eukaryotes differ from the prokaryotes (including the
archaebacteria) not only by the possession of a nucleus and
*mitosis but also by individual protein-rich chromosomes,
*meiotic sexuality (including viable regular cell fusions),
cellular organelles, highly complex sets of regulatory genes, and
all those genes that permit biodiversity... When a biologist
speaks of eukaryotes, he or she has in mind palms, oaks, and
orchids; mice, bats, and whales; and hummingbirds, chickens, and
ostriches. And this world of highly evolved eukaryotes is simply
an entirely different world from the world of the two kinds of
bacteria, the Prokaryotes. 3) Ranking, in any scheme of
classification of items (living or not), is by necessity based on
degree of difference. The two kinds of bacteria, in the vast
majority of their characteristics, are exceedingly similar to
each other and fundamentally so different from the eukaryotes
that they have to be ranked as a single *taxon, the prokaryotes,
different from the only other taxon of this rank, the eukaryotes.
Mayr suggests that only a two-empire classification correctly
reflects this structure of the living world.

-----------
E. Mayr (Harvard University, US)
Two empires of three?
(Proc. Natl. Acad. Sci. US 18 Aug 98 95:9720)
QY: Ernst Mayr <emayr@oeb.harvard.edu>

-----------
Text Notes:

... ... *habitats: Many species of archaebacteria live in hot
acidic conditions, growing best at temperatures approaching 100
degrees centigrade. Because of this, it has been suggested the
lineage is more ancient than eubacteria, arising during
primordial conditions on Earth.

... ... *mitosis: In this context, division of the cell nucleus.

... ... *meiotic sexuality: A reduction division process whereby
a nucleus divides by 2 divisions into 4 nuclei, each containing
half the original number of chromosomes.

... ... *taxon: The organisms comprising a particular taxonomic
entity.

-------------------
Summary & Notes by SCIENCE-WEEK <http://scienceweek.com> 25Sep98
For more information: http://scienceweek.com/swfr.htm

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