Evolutionary Theory





Evolutionary Theory
A theory of changes in organic design through
controlled random mutations and contingent selection
(Francis Steen, revised 25 March 2001)


--------------------------------------------------------------------------------

The Neo-Darwinian Synthesis
In broad terms, contemporary evolutionary theory builds on the
synthesis of Darwin's ideas of natural variation and selection and
Mendel's model of genetic inheritance accomplished by R.A. Fisher,
J.B.S. Haldane, and Sewall Wright in 1930-32. For an overview, see
George Williams, Evolution and Natural Selection (1966).

The Unit of Selection. The central realization of the neo-Darwinian
synthesis is that natural selection is best understood to be acting on
variation among elements that persist. Thus, natural selection does not
act on me as an individual, because when I die, the structures that
constitute my body and my genome - my full complement of genes - break
down. Nor does it act on collections of individuals, since each of
these eventually suffer the same fate (though see below).

However, if I have children, some of my genes persist, and it is here
we must look for the appropriate unit of selection. The genome is
organized into chromosomes that come in pairs. Each pair contains
functionally similar but not identical alleles at corresponding loci.
In the process of meiosis, sperm cells or eggs (gametes) are generated
that contain single chromosomes instead of pairs. Each single
chromosome is made up of alleles from both members of the pair in what
appears to be a random shuffle.

Thus, the chromosome does not persist, but is scrambled with elements
of its paired partner in the process of meiosis. This is repeated for
each generation. What persists is the allele, which can be defined
simply as a stretch of genetic material that is not broken up in the
shuffle of meiosis, but is transmitted intact into the gamete and thus
into the next generation.

Natural Selection. Once in the fertilized egg, the alleles regulate the
construction of the organism. If this project is not successful, or if
the organism lives but does not reproduce, all the alleles perish
together. If there is even the slightest causal link between the
failure to reproduce and a particular allele - that is, if a variant
allele at the same locus in another organism enabled that organism to
reproduce - then natural selection can be said to be operating on that
allele. Such weak causal links can be detected by examining the
reproductive outcomes of populations with slightly different phenotypic
features; for an illuminating example, see Jonathan Weiner's The Beak
of the Finch: The Story of Evolution in Our Time (1994). Evolution,
accordingly, can be defined as a change in allele frequencies in a
population.

The Strength of Selection. The selective survival of individual
organisms due to functional differences, and thus the differential
transmission into the next generation of alleles, is a pervasive force
shaping the trajectories of evolutionary lineages. Natural selection
takes several forms--directional, stabilizing, disruptive,
indirect--and its strength varies in acting on different organismal
traits. In the last several decades, researchers have attempted to
measure the strength of the various types of natural selection,
studying its effect on phenotypes and individual traits of organisms in
the wild and in the laboratory. Kingsolver et al. examine this
literature and find some unexpected patterns:

In both vertebrates and plants, the strength of selection on
morphological traits was twice as great as on life-history traits.


The strength of selection on some components of fitness such as
fecundity or mating success was greater than on others such as survival


The strength and frequency of stabilizing selection, which keeps a
trait constant, was no greater than that of disruptive selection, which
favors change.
Kingsolver, JG; Hoekstra, HE; Hoekstra, JM; Berrigan, D; and others
(2001). The strength of phenotypic selection in natural populations.
American Naturalist 157. 3 (Mar 2001): 245-261.

Variation. For natural selection to operate, alleles that can occupy
the same locus in the genome must differ somewhat between individuals.
Such variation can appear because of replication or transcription
errors, because of damage by radiation, or from other causes. Since the
problem space of an organism is theoretically infinite, a random system
of variation would be useful, though it need not be the only mechanism.
For instance, regulatory genes that code for the introduction of random
errors in specific alleles in response to certain environmentally
generated cues may survive and spread.

Some evolutionary biologists argue that mutation rates are too slow to
account for the observed variation. Since the functional effect of an
allele depends on its position - the same allele at a new locus can
subtly or dramatically alter the action of a whole suite of genes - it
is possible that the primary cause of variation is chromosomal
recombination rather than mutation (see McClintock 1987). Mutations in
regulator genes is another candidate for rapid change (see King &
Wilson 1975).

It is now also looking increasingly likely that the genome has evolved
strategies of mutation (see Pennisi 1998 for an up-to-date discussion).
If this turns out to be the case, mutations may still tap into the
random, but the random may be tapped at controlled points so that the
overall outcome is far from random. Localized novelties can be
incorporated into the genome in non-random ways. Since random changes
in a complexly ordered system may have moderately predictable outcomes,
there is a vast field of possible genetic strategies that may evolve in
response to patterns in the results of random mutations at determinate
sites in the highly ordered genome. Life in this sense may be said to
actively feed on the random in a controlled manner.

Somatic hypermutation. In an interesting special case, medical
researchers have found that the immune system engages in a process
called somatic hypermutation to increase antigen receptor diversity. In
the body's immune response, B-cells are responsible for manufacturing
and secreting antibodies, the protein molecules that bind to antigens.
The ability of the immune system to recognize and respond to the
enormous number of antigens encountered by an individual in a lifetime
is due in large part to the diversity of antibodies (immunoglobulins)
produced by B-cells. Each B-cell produces only a single species of
antibody, and during the systemic immune response, the presence of a
specific antigen results in the proliferation of B-cells producing
antibody specific for that antigen (clonal selection). Antibody
diversity depends on variability in the constituent amino acid
sequences, made possibly by somatic recombination - a scrambling and
reassembly of genes - in the DNA of the B-cell. During the past 15
years, it has become evident that in immune system B-cells, the part of
the genome coding for the variable parts of antibodies is involved in a
process of "hypermutation", a substantial increase in mutation rate,
the effect of which is to provide the immune system with a rapidly
changing enormous library of possible antibodies. This hypermutation
process is highly specific to the immune system, and it occurs only
within a DNA segment of approximately 1000 to 2000 DNA bases, the
segment that encodes the bulk of the variable regions of the antibody
polypeptides. The mechanism of the hypermutation process remains
unknown. Since B-cells pass directly to the offspring from the mother,
somatic hypermutation in the immune system provides a special case of a
Lamarckian mechanism of inheritance. For an early overview, see French
et al (1989).

Epistemological considerations. There is no reason to think we have a
complete understanding of the operation of the genes. There are central
areas of genetics, such as the question of how genes build bodies, that
are still very poorly understood. It is also implausible that we have a
full understanding even of those genetic processes for which we have
highly specified models and vast amounts of experimental data
supporting these models; this limitation is simply due to the inherent
limitations in the activity of knowledge (see No Final Theory: Science
as Perception). Such chronic incompleteness is a reason to be open to
the discovery of new levels of order in the operation of the genes in
ontogeny and under natural selection, to improved definitions of the
scope of current models, and to a clarification of the mechanisms at
work.

Current debate. There are various grounds on which to question aspects
of the current evolutionary model, and a lively debate persists today.
Evolution is in principle hard to model precisely, since the changes it
describes usually takes place over time periods that are inaccessible
to human beings. Consider the related situation in astronomy. Changes
in the movement of the stars are slow, and until very recently were too
slow to be detected within the lifetime of an individual. However, with
the help of a continuous series of observations dating back to the
fifth century BC, Copernicus was able to formulate a detailed model
that fit two thousand years of data. Unfortunately, in the case of
biology, two thousand years of continuous observation would in most
cases reveal very little. We must thus rely in indirect evidence, such
as fossil remains and systematic structural similarities and
differences in living forms. This evidence leaves room for a variety of
possible interpretations of past events, and thus of the mechanisms of
change that underlie them. I can examine only a few focal points of
contention.

Gradualism. All the way back to Darwin, the notion that changes accrue
gradually over long periods of time has been a central proposition of
evolutionary theory. As Ernst Mayr put it in Animal Species and
Evolution (1963), "all evolution is due to the accumulation of small
genetic changes" (p. 586).

In contrast, the fossil record suggests long periods of stasis followed
by brief periods of rapid change - what Niles Eldredge and Stephen J.
Gould dubbed punctuated equilibrium. This data has sometimes been taken
as evidence against the neo-Darwinian model by people who believe the
order of nature is due to the intentional act or acts of a supernatural
being. Within the scientific tradition, the relative lack of continuous
change in the fossil record is interpreted as evidence that speciation
events have typically taken place in small populations over relatively
short periods of time.

In addition, gradualism should not be discounted. For instance, in the
period from 300,000 to 100,000 year ago, fossil remains of the genus
Homo show a wide range of forms. It is not unlikely that we have
inherited alleles from individual mutations that took place over a wide
geographical area during this period. As the best mutations spread
throughout the existing populations, the range of functionally
meaningful variation drops towards zero. Archeologists of the future
may well see only our remains, appearing as if by the hand of God,
while the gradual accumulation of alleles that made us possible leaves
little or no trace.

Group selection. There are situations where it is useful to think of
natural selection acting on collections of alleles rather than on
individual alleles, and thus on individuals, groups, species, and taxa.
In most cases, however, group selection is thought to be so weak that
the effect can be ignored; for a sustained argument, see Williams
(1966). In contrast, David Sloan Wilson (2000) points out that
"Group-level adaptations will evolve whenever group-level selection is
stronger than individual-level selection" and argues this is often the
case. Darwin, he points out, held that "the driving force behind the
evolution of morality was the process of more moral groups replacing
less moral groups, not the process of more moral individuals replacing
less moral individuals within groups." He concludes that "group
selection is a significant evolutionary force in nature and especially
strong in the case of our own species." This article, a review of
Wright's Nonzero, provides a useful overview of the debate.

Chris Boehm (1999) has proposed that group selection may have acted to
create psychological adaptations favoring egalitarianism; see extracts.


Litterature on group selection

Boehm, Christopher (1999). Hierarchy in the forest: the evolution of
egalitarian behavior. Cambridge, MA: Harvard University Press. Extracts
(local), publisher's presentation (external) and editorial reviews
(Amazon.com). Reviewed by Vincent Kiernan (external).

Keller, Laurent (ed.) (1999). Levels of Selection in Evolution.
Princeton, NJ: Princeton University Press. Reviewed by Herbert Gintis
(Amazon, external).

Wilson, David Sloan and Elliott Sober (1994). Reintroducing group
selection to the human behavioral sciences. Behavioral and Brain
Sciences 17. 4 (December): 585-609.

Wilson, David Sloan and Elliott Sober (1998). Unto Others: The
Evolution and Psychology of Unselfish Behavior. Cambridge, MA: Harvard
University Press

Wilson, David Sloan. A review of Wright, Nonzero. Full text (external).



Baldwin effect. A longstanding evolutionary principle called the
Baldwin Effect says that an advantageous behavior, once it has appeared
in a population, will gradually reshape the genes of the species which
has adopted it.

"At the end of the 19th century, biologist J. M. Baldwin enunciated the
Baldwin Effect, which observed that when a species learns a useful new
skill, the addition to its behavioral repertoire will reshape its
biology. Over time, says Baldwin, natural selection will bless the
members of ensuing generations whose limbs and brains are suited to the
maneuver, and cull out those whose anatomy is ill-suited to the
innovative gambit." (Steven Levy, Artificial Life. New York: Vintage,
1993, p. 265.)

Literature on the Baldwin effect

Baldwin, J.M. (1896). "A new factor in evolution." American Naturalist
30: 441-451. Full text (external).

Behera, N. and V. Nanjundiah (1995). "An investigation into the role
of phenotypic plasticity in evolution." Journal of Theoretical Biology
172: 225-234

Belew, Richard K. and Melanie Mitchell, eds. (1996). Adaptive
Individuals in Evolving Populations: Models and Algorithms. Reading,
MA: Addison-Wesley. Series title: Proceedings volume in the Santa Fe
Institute studies in the sciences of complexity, v. 26.

French, R. and A. Messinger (1994). "Genes, phenes and the Baldwin
effect." Artificial Life IV, ed. Rodney Brooks and Patricia Maes.
Cambridge, MA: MIT Press.

Hirst, Tony. "Search Space Neighbourhoods as an Explanatory Device:
General Observations and a Reconsideration of the Baldwin Effect."
Abstract.

Smith, John Maynard (1987). "When learning guides evolution." Nature
329: 761-762.

Turney, Peter, Darrell Whitley, and Russell Anderson (eds) (1997).
"Evolution, Learning, and Instinct: 100 Years of the Baldwin Effect."
Evolutionary Computation (Special Issue on the Baldwin Effect), vol. 4,
no. 3. Abstracts (external).

Weber, Bruce and Soren Brier (eds.) (2000). The Embodied Mind and the
Baldwin Effect. Special Issue of Cybernetics and Human Knowing 7. 1.
Publisher's presentation (external).

Non-linear dynamics. The realization that even mechanical systems are
subject to non-linear dynamic effects may have important consequences
for biology. For an overview, see Stuart A. Kauffman, The Origins of
Order: Self-organization and Selection in Evolution (1993); here is a
brief excerpt:

"If the origin and evolution of life is like an incomprehensible
computer algorithm, then, in principle, we can have no compact theory
that predicts all the details of the unfolding. ...I suspect that
evolution itself is deeply like an incomprehensible algorithm. If we
demand to know its details, we must watch in awed wonder and count and
recount the myriad rivulets of branching life.... we are not precluded
from the possibility that many features of organisms and their
evolution are profoundly robust and insensitive to details. If, as I
believe, many such robust properties exist, then deep and beautiful
laws may govern the emergence of life.... We can never hope to predict
the exact branchings of the tree of life, but we can uncover powerful
laws that predict and explain their general shape."
Consciousness and ethics. The basic explanatory framework of the
neo-Darwinian synthesis is materialist (see for instance excerpts from
Williams (1966). If this framework is adhered to, the phenomena of
sentience and value must remain epiphenomenal. It is not clear this is
a fully satisfactory situation, nor do we have any a priori reason to
believe that the materialist framework is adequate for all phenomena.
However, it is important to realize that the incompleteness of
evolutionary theory is not in itself an endorsement of other modes of
thinking we find easier to believe in. Rather, it may in general be
inappropriate to use a theory of any kind as an ultimate framework for
life as a whole. See for instance Bohm and Wiley on knowledge as
perception.

--------------------------------------------------------------------------------

Some basic principles of evolutionary theory
the principle of self-replication: living forms are autocatalytic and
self-replicating material processes (phenotypes)
the genetic principle: the construction of the phenotype is made
possible by chemically stored information (genotypes)
the principle of randomness: the genotype is subject to changes by
virtue of its material composition that lead to random changes in the
information stored
Some entailments
random variation: random mutations in the genotype will generate
randomly different phenotypes
contingent selection: some mutations will prevent the organism from
replicating in its environment while others will facilitate replication

non-teleological design: the process of evolution itself is not
designed to yield a specific result, although it results in organisms
able to perform specific functions
Definitions
reproductive fitness: the statistically likely potential or actual
number of reproductively viable offspring of an organism
adaptation: the specific phenotypic result of a mutation that is
favored by selection
allele: the smallest genetic unit that is sufficient to code for a
given adaptation
evolution: changes in allele frequencies in a population
Mechanisms of Selection
natural selection: all factors in the environment that influence allele
frequency distributions, of which the following are special kinds
sexual selection: an adaptation whereby organisms select sexual
partners on the basis of specific cues
kin selection: an adaptation whereby organisms devote resources to
increase the reproductive fitness of their relatives, in proportion to
their relatedness
Historical Notes

Before Darwin: Invertebrate Paleontology as Geology

"Little work of importance was done in paleontology until the 1700's,
at which time both vertebrate and invertebrate fields began to assume
importance. Intensive work in the invertebrate area arose from
recognition of the fact, first clearly seen by William Smith, an
English civil engineer and amateur geologist of the period, that a
given set of beds tended to contain the same species of shells over
vast and widely separated areas. Accurate determination of fossils
could thus be of great practical use to the stratigrapher; as a result,
invertebrate paleontology tended to develop not as an independent
science, but as a handmaiden to the geologist -- a working tool for the
stratigrapher looking for oil or ores or coal. The fossil shells were
rarely thought of as the remains of once-living organisms, but merely
as convenient markers for the identification of successive formations,
and would have been as useful had they been identifiable mineral
inclusions or distinctive assortments of nuts and bolts...

With this background, the invertebrate workers of Darwin's day not
merely lacked interest in evolutionary ideas, but were inclined to view
them with suspicion as detrimental to their work. For clear-cut
stratigraphic work, the species in a given formation should be stable
entities, clearly distinguishable from those in the strata above and
below. The idea of gradual change and of transitional forms was
abhorrent...

With this to contend with, it is apparent why Darwin was thrown on the
defensive in his treatment of the fossil record. He could not call on
the paleontologists for support; the most he could do was to attempt
appeasement, to show that it was at least possible to interpret the
geological story in evolutionary terms, and that there was no
insuperable objection."

-- A.S. Romer: "Darwin and the Fossil Record" (1958). In S.A. Barnett
(ed.). A Century of Darwin. From chapter 6.


.