• Lecture notes:
• A demonstration of natural selection in vitro (experiments described by Leslie Orgel)
• Darwin's discussion of natural selection
• Exercises
• Simulations

I.  How natural selection works

A.  Natural selection is really a result of any system that has:
1.  Heredity (i.e., the ability to pass traits on to offspring)
2.  Reproduction (i.e., the ability to multiply and thereby increase population size)
3.  Variation (i.e., differences in heritable traits that affect "Fitness" = the ability to survive and reproduce)

B.  A demonstration in vitro (Orgel, 1979)

• Required reading:  Leslie Orgel.  1979.  Selection in vitro.  Proc. R. Soc. Lond. B 205:435-442.  (On reserve in Bobst Library.)

1.  The Qb system and previous observations
     a.  Variation:  Error rate of the replicase
     b.  Reproduction:  Replication exponential with excess enzyme and nucleotides
     c.  Heredity:  Using free nucleotides and template, replicase copies strands

2.  Experiment 1:  Selection for drug resistance
     a.  Successive transfers of "V2 RNA" with drug (or without = control)
     b.  Rates of nucleotide incorporation were measured at each transfer
     c.  At different intervals, increase the concentration of drug
     d.  Successive strains tested for their ability to replicate in the presence of drug
     e.  Successive populations also tested for the nature of the adaptation

3.  Experiment 2:  The molecular basis of the adaptation
     a. Again, selected for drug resistance, but kept drug concentration constant
     b. Evolution eventually stopped!
     c. The 3 changes occurred successively
     d. The 3 changes occurred reproducibly in the same stepwise order
     e. The nature of the changes depended on the conditions

4.  Conclusions
     a.  If the conditions remain constant, evolution eventually stops
     b.  A population of entities that Multiply, Vary and have Heritability can Evolve and Adapt
     c.  Natural Selection produces improbable results (reduces improbability)
     d.  The process is analogous to hill-climbing

(See also Dawkins' Chapter 3 for further demonstrations of this nonrandom mechanism.)

• Optional reading:  Daniel C. Dennett.  1995.  Darwin's dangerous idea:  Evolution and the meanings of life.  Simon & Schuster, New York.  ISBN 0-684-80290-2 (call no. QH375.D45; also placed on reserve in Bobst Library)).  The first part presents a meticulous reconstruction of Darwin's "algorithm", an introduction to the profound effect of Darwin's new way of thinking on western philosophy, and extensions of the application of this algorithm back through the origin of life to the "beginning(s)" of the universe.

II.  Darwin's discussion of Natural Selection

A.  Variations DO occur naturally

1.  Variations have occurred (in recorded history) that were "useful"
2.  Expect different types of variations
     a.  Advantageous
     b.  Deleterious
     c.  Neutral
3.  Not a lot of variation is required-variation can be imperceptible

B.  Some features of Natural Selection

1.  Selection is best exemplified when conditions are changed
2.  Adaptations are not perfect
3.  Natural Selection is comparable to Artificial Selection, except that it's more powerful (more sensitive to finer variations)
4.  Its effects are barely perceptible, except over long periods of time
5.  Because of the Correlation of Growth, selection on one character may affect another
6.  Even if a structure is used only once in an organism's life, it can be subject to strong selection
7.  Natural Selection cannot modify the structure of one species for the exclusive benefit of another species

C.  Sexual Selection explains several bizarre and unique features of organisms (esp. males) as Adaptations

D.  Several hypothetical scenarios demonstrate the action of Natural Selection in the evolution of Adaptations

1.  Predator-prey relationships (wolves and deer)
2.  Experiments on insect pollination to explain flower structure as Adaptations
3.  Applies the Uniformitarianist Principle to Natural Selection to explain larger modifications (p. 95)

E.  Evolution of Sex as an Adaptation

1.  Selection against the results of inbreeding (Darwin's rationalization)
2.  Evidence that Sex is an Adaptation:  Even in self-fertilizing plants, there are often special adaptations that ensure crossing
3.  Animals usually have different sexes, but some are self-fertilizing hermaphrodites, which DO occaisionally cross
4.  Darwin predicted that exclusive self-fertilization (and he would probably include exclusive asexual reproduction) would not produce a long-lived lineage

F.  Circumstances favorable to Natural Selection causing change

1.  Reduced intercrossing between differet varieties
2.  Rapid rate of population growth
3.  Isolation
4.  Large Areas produce more species that endure longer

G.  The Process is usually slow

1.  Depends on environment, in which changes are slow
2.  Arisal of variation may be slow
3.  Retarded by intercrossing
4.  Slowness accords well with the geological record
Despite this slowness, still more powerful (sensitive) than Artificial Selection

H.  Extinction is a part of the process

1.  Due to Natural Selection, some forms increase, others decrease
2.  Because the total number of forms on Earth remains constant, and New Forms are continuously produced, Extinction is inevitable
3.  The most closely-related competitors will generally suffer the most

I.  Types of Selection

1.  Directional
2.  Stabilizing
3.  Disruptive, Diversifying (important to Darwin's view of branching evolution)

J.  "Divergence of Character" (see Darwin's only Figure)

1.  Variation originates as slight differences, and Natural Selection gradually augments these differences
2.  Diversification is advantageous because it allows more resources to be utilized
3.  Natural Selection thus explains branching evolution (according to Darwin)

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1. In the experiment that Orgel describes, populations of RNA molecules are sampled and successive transfers are made into new media.  Because there are always plenty of resources for replicating RNA templates, the carrying capacity is never reached; so there should be no "Struggle for Existence"--or is there?  How does natural selection work in this case?  What features of such a case allow the replacement of one variant by another?
    
2. Why was the experiment that Orgel described repeatable if variation is supposed to be random?  Why did the 3 changes occur in the same order each time the experiment was repeated?  Why does this not support an orthogenetic mechanism of evolution (or does it)?
    
3. Why should evolution stop in the experiment that Orgel described if variation is supposed to appear continually?  Would you necessarily expect evolution (e.g., of the RNA sequence) to cease altogether if some variations did not affect "fitness" per se (i.e., if such variations were "neutral")?
    
4. There is no sex in the experimental system described by Orgel (i.e., there is no recombination between different variants).  How might the introduction of recombination into this system affect the results?  What might this imply about the origin and maintenance of sexual systems?
    
5. Why does Darwin suggest that adaptations are not predicted to be "perfect", despite such incredibly "well-designed" features as hawk eyes, bat sonar, insect wings and human brains?
    
6. Why should the process of change due to natural selection be retarded by intercrossing?  if this is the case, then how can different species possibly arise from a single ancestral species?
    
7. Explain how each circumstance listed above in item II F should be "favorable to natural selection".
    
8. Calculate the probability of rolling "box cars" (a pair of sixes) with a pair of dice.  Now roll the dice--how many rolls does it take you to get "box cars" the first time?  Repeat the experiment 10 times.  Now use a form of the algorithm of natural selection:  the first time you roll a six on either die, keep it, and roll the second die until you get a second six.  What is the probability of getting "box cars" under these "rules" of natural selection?  Repeat the experiment 10 times.  How does "natural selection" reduce the probability of getting a rare result?  Increase the number of dice to 4 and repeat your calculations.  How is natural selection being modeled by this experiment (e.g., what do the dice represent)?
    

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The following links provide simulations that demonstrate how natural selection (a result of the differential reproduction of variants) results in "adaptations" (i.e., adaptations to your particular whims of what constitutes an interesting-looking graphic).  You will also find that selection often results in evolutionary change (even if selection occurs unconsciously or randomly!). 

While you are "playing" the simulations, try to ask yourself what principles are being demonstrated, what might be the underlying assumptions and limitations of the model, and if there are other processes or components of biological reality that are not being modeled by the simulations.

• An online rendition of Richard Dawkins' "Blind Watchmaker"

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