Evolution Notes

Evolution: The Universal Laws in Biology

"Nothing in biology makes sense except in the light of evolution." - Theodosius Dobzhansky, 1973

Biology vs. Physics/Chemistry

Biology is distinct due to natural selection and evolutionary history.
Physics and chemistry differentiate elements (e.g., copper vs. iron).
Biology differentiates organisms based on sex (e.g., males vs. females).

Scientific Inquiry: How and Why

Descriptive questions: what, where, and when.
"How" questions: proximate, mechanistic explanations.
"Why" questions: ultimate, evolutionary explanations.

Snail Shell Example

Two snail groups with different shell characteristics (hard/thick vs. soft/thin).
Physicochemical properties of the shell's materials permit the observed characteristics but don't fully explain them.

Evolution as a Way of Thinking

Evolution is not just a biological theory but a perspective applicable to everyday life.

History of Evolutionary Theory

Fixed Species Concept

From classical times through the Renaissance, species were considered fixed and unchanging.

Fossils and Strata

Late 18th century: Geologists like William Smith discovered that past species differed from present ones based on rocks and fossils.

Transmutation

Around 1800, scientists (e.g., Erasmus Darwin) started considering that species might change or transmute.

Jean Baptiste de Lamarck

Proposed that animals could change or transmute.
Proposed that characteristics acquired during an animal's lifetime could be passed to offspring.
Example: Giraffes developed long necks through generations of straining to reach high branches.

Inheritance of Acquired Characteristics (IAC)

Lamarck's proposed mechanism for evolution.
Suggested that modifications to organisms during their life could be inherited by their offspring.

August Weismann

Disproved Lamarck's theory through the tail-chopping experiment on mice (1889).
Cut off the tails of hundreds of mice for 22 generations.
Conclusion: Changes to the body during an individual's lifetime do not affect the reproductive cells or the offspring.

Information Flow: DNA to Phenotype

Information to build a body is stored in DNA, which, influenced by the environment, determines the phenotype.
Conventional wisdom: Changes to the phenotype during life do not affect the DNA sequence.
Information flow is primarily one-way: DNA -> phenotype.

Paul Kammerer and the Midwife Toad

Kammerer's experiment (1920s) involved midwife toads (which typically mate on land and lack nuptial pads).
He forced these toads to mate in water, supposedly resulting in the development of nuptial pads, which were then inherited by offspring (Lamarckian inheritance).
Claimed that toads mating in water would eventually acquire pads, and offspring would inherit pads via Lamarckian inheritance.

Epigenetics

Study of mechanisms controlling gene activity in time and space during organism development.
Heritable changes in gene expression caused by mechanisms other than changes in DNA sequence.
The DNA sequence isn't changed, but gene expression levels can be altered, and these changes may be inherited.
Epigenetic changes are preserved when cells divide, but most occur within one lifetime.
Epigenetic changes in sperm or egg cells can be inherited.
Environmentally induced methylation (addition of a methyl group - $CH_3$ - to cytosine nucleotides) can cause epigenetic effects.
More heavily methylated regions are transcribed less frequently.

Epigenetics - Dutch Study

Dutch winter famine (1944/45) example of epigenetic effects.
Children of pregnant women during the famine were born smaller.
Grandchildren were also born smaller than average, suggesting famine-induced epigenetic changes were passed down.

Epigenetics - Mouse Studies

Two papers published in 2014:
- In Utero Undernutrition in Male Mice Programs Liver Lipid Metabolism in the Second-Generation Offspring Involving Altered Lxra DNA Methylation.
- Implication of sperm RNAs in transgenerational inheritance of mediate non-Mendelian inheritance of traits or phenotypes acquired across life. sncRNAs are abundant in the mature sperm in mammals and may therefore convey transgenerational inheritance effects of early trauma in mice early traumatic stress and contribute to associated pathological traits.

Obesity, Type 2 Diabetes, and Epigenetics

Heritable components of obesity and type 2 diabetes may be due to epigenetic mechanisms.
Intrauterine growth restriction (IUGR) in mice due to malnutrition leads to obesity and glucose intolerance in offspring and subsequent generations.
IUGR results in epigenetic modifications in germ cells transmitted to somatic cells, influencing health and disease risk.

Vestiges of the Natural History of Creation

Published anonymously by Robert Chambers in 1844.
Very popular, prepared the public for Darwin's theory.

Charles Darwin (1809-1882)

Published "On the Origin of Species" in 1859.
Son of a wealthy doctor, dropped out of medical school.
Studied theology, interested in natural history.
Served as captain’s companion on The Beagle.
Wealthy and never had to work.

Voyage of the Beagle (1831-1836)

Darwin was the companion for Captain Fitzroy.
The Beagle's mission was to map the coast of South America.
Traveled around the world, including the Galapagos Islands.
Galapagos Islands consist of volcanic islands off the coast of Ecuador.

Galapagos Islands

Unique animals include giant tortoises, marine iguanas, and Darwin's finches.

Influence of Geological Thinking on Darwin

Darwin read Lyell's "Principles of Geology."
Lyell emphasized:
- Gradualism: Geological features are explained by slow, gradual processes (e.g., erosion).
- The Earth is very old, allowing ample time for change.

Darwin's Observations

Different faunas in similar habitats in different parts of the world.
Unique island faunas resembling those on adjacent land masses.
These observations suggested species change over time (evolution).

Influence of Malthus on Darwin

Darwin read Malthus’ essay on human population growth.
Malthus' idea: Human population grows faster than the food supply.
Competition for food results in the survival of the fittest.
Darwin applied this to all life, developing the concept of Natural Selection.

Natural Selection

Darwin proposed in "Origin of Species" (1859) how one species could give rise to another.
Limited food leads to competition and survival of the fittest.
Natural selection of the best-adapted individuals leads to evolution of new species.

What is Evolution?

Darwin: Descent with modification (changes occur over generations) due to natural selection.
Modern: Change in allele (gene) frequencies over time due to natural selection and other factors.

Body Mass of Hornworms

Manduca sexta larvae grow from 1 mg to ~12 grams (15,000 fold) in ~30 days.
Ideal model animal for studying growth since the 1960s.

Dramatic Over-Simplification Example

Frequency example (rabbits):
- Initial: 1/10 = 10%, then 3/12 = 25%, then 9/18 = 50%
- After 5 generations: 81 black rabbits, 9 white rabbits, Frequency of black is (81+9)/90 = 90%.
- Evolution occurs.

Evolution by Natural Selection (Darwin's 4 Postulates)

There is variation in populations.
Variation is heritable.
Some organisms are more successful at surviving and reproducing (differential reproductive success).
Non-zero correlation between traits and reproductive success. Organisms with the best characteristics are naturally selected.

Natural Selection and Reproduction

Traits with no correlation with reproduction will not be selected.
Reproduction is paramount.
Natural selection doesn't affect anything after reproduction.

Darwinian Fitness

Ability of an organism to survive and reproduce in its environment.
Fitness is measured relative to others of its species, not across different species.

Darwin's Contribution

Spent over 20 years developing his ideas and gathering evidence.
In 1858, Charles Darwin and Alfred Russel Wallace jointly proposed natural selection.
In 1859, Darwin published "On the Origin of Species."

Bishop Wilberforce vs. Thomas H. Huxley

Evolutionists won the debate, but Darwin’s idea of Natural Selection was not immediately accepted.

Darwin's Troubles

The Idea of evolution was rapidly accepted by scientists.
Lack of understanding of heredity and population genetics prevented natural selection being accepted as the principal mechanism of evolution until 1930’s.
Darwin did not know: what causes variation and how phenotypes get passed on.

Pangenesis

Darwin posited that atomic sized gemmules formed by cells would diffuse and aggregate in the reproductive organs and then be transmitted from parent to offspring.
Galton’s experiments on rabbits showed that this was not true.

Genetics

Gregor Mendel (1856-63) cultivated 29,000 pea plants.
He figured out the basic principles of genetics.
Mendel’s work only came to light in 1900, long after his death.

Modern Synthesis

Early 20th century: scientists made sense of how evolution worked.
Building on Mendel's genetics, studies showed how characteristics in a population could be selected by environmental pressures.
Julian Huxley termed this the Modern Synthesis, bringing Darwin's Natural Selection back to the center of evolutionary theory.

The Modern Synthesis

ca. 1930 – 1950
Incorporation of population genetics theory into evolutionary biology
Geneticists/Statisticians: – R. A. Fisher, Sewall Wright, J.B.S. Haldane
Evolutionary biologists: – Th. Dobzhansky, George Gaylord Simpson, Ernst Mayr, G. Ledyard Stebbins

The Modern Synthesis

Gradual evolution results from small genetic changes that are acted upon by natural selection (and other factors—more details later)
The origin of species and higher taxa (macroevolution) can be understood as selection acting on individuals (microevolution) over long periods of time.

Genotype vs. Phenotype

The genetic make-up of an organism is known as its genotype.
Organism’s genotype and the environment in which it lives determines its total characteristic traits i.e. its phenotype.

Mutation

Occasional mutations or copying errors occur when DNA is replicated.
Mutations may be caused by radiation, viruses, or carcinogens.
Mutations are rare and often have damaging effects. Consequently organisms have special enzymes whose job it is to repair faulty DNA. The repair processes cost resource and energy (more later).

Variation

Nevertheless, some mutations will persist and increase genetic variation within a population.
Variants of a particular gene are known as alleles.

Natural Selection

Mutant alleles spread through a population.
If an allele exerts a harmful effect, it will reduce the ability of the individual to reproduce and the allele will be removed from the population.
In contrast, mutants with favorable effects are preferentially passed on

Application of Evolutionary Theory

Computer science
Economics
Politics
Medicine
Psychology
Social science

How Evolutionary Theory Makes Street Life Better

Evolution of dark skin and agriculture
Evolution of Indo-European language and lactose tolerance
Why my son hates green vegetable?
Being fat is not my fault!

Evolutionary Algorithm

Initialization
Mutation & crossover
Inheritance
Selection
Reproduction
Termination
In an EA, a population of strings (genotypes), that encode candidate solutions (phenotypes) to an optimization problem, evolves toward better solution.

Economics and Political Science

Game theory
Evolutionarily Stable Strategy (ESS) (Nash equilibrium)
ESS is a strategy that is stable, so that natural selection prevents alternative (mutant) strategies from invading successfully.

Hawk vs. Dove Strategy

Hawk: always fight as hard as they can, retreating only when seriously injured.
Dove: merely threaten never hurting anybody.
If a hawk fights a dove: dove runs away.
If a hawk fights a hawk: one win, the other one seriously injured.
If a dove fights a dove: nobody gets hurt; they go on posturing at each other for a long time until one of them tires or decides not to bother any more, and therefore backs down.
50 pts for a win, 0 for losing, -100 for being injured; -10 for wasting time over a long contest. (The points are made up. They are like gene survival. Individual with higher points leaves many genes behind him in the gene pool—fittest).

Hawk vs. Dove - Averages

All doves: Average = 15 points
When a hawk gene mutation happens, Hawk = 50 points (Advantage over dove).
Hawk genes spreads.
If everyone is a hawk, Average = -25 points.
When dove mutation happens, Average = 0 points (Higher than hawk).
Dove gene spreads.
Stable Ratio = 5/12 doves to 7/12 hawks

Evolutionarily Stable Strategy (ESS)

Once an ESS is achieved it will stay: Natural Selection will penalize deviation from it. (The mutant gene will not spread too far).

Evolutionary Medicine

Application of evolutionary principles to understand health and disease.

Evolutionary Psychology

An approach to the psychological sciences in which principles and results drawn from evolutionary biology, cognitive science, anthropology, and neuroscience are integrated with the rest of psychology in order to map human nature.
The functional components that comprise human nature were designed by natural selection to solve adaptive problems faced by our hunter-gatherer ancestors, and to regulate behavior

Cultural Evolution

Meme and gene.
A meme is a cultural idea.
Like genes, memes cause "phenotypes".
Propagate through transmission from one host to another.
The contents and implications of a certain idea influence its likelihood of being copied.
Can have mutations
Differential reproduction sets up natural selection
Coevolution of meme and gene (e.g. Catholics’ idea of large family)

Deep Origins of Britain’s Industrial Revolution

For centuries the wealthier British had left significantly more surviving children than their poorer compatriots, leading their offspring to constitute an ever larger share of each generation
The near-Malthusian poverty of ordinary English life during this era meant that the impoverished lower classes often failed even to reproduce themselves over time, gradually being replaced by the downwardly mobile children of their financial betters.
Since personal economic achievement was probably in part due to traits such as diligence, prudence, and productivity, these characteristics steadily became more widespread in the British population, laying the human basis for later national economic success.

Evidence for Evolution

Artificial Selection

Chapter 1 of The Origin of Species

How it works

Breeders choose individuals that have desirable characteristics to be the parents of the following generations (i.e., breeders are the selective agent and the characters that they use to chose parents are the targets of selection).
These parents then artificially have higher reproductive success.
If the selected trait is heritable then the breed or variety will come to express the selected trait to a greater degree, or completely new breeds and varieties can be created
Examples: Darwin's pigeons, Goldfish, Peach, Watermelon, Corn.

Vestigial Structures

A useless body part that has an important function in other closely allied species.
Darwin’s argument: Creation v.s. evolution
Reduced wings in flightless birds (e.g., kiwi)
Reduced or missing eyes in cave organisms (e.g., Mexican tetras)

Jerry-Rigged Structures

Jerry-rigged structures e.g. the Panda’s thumb.
In pandas, a wrist bone has been modified into a "thumb" that is used to grip bamboo stalks and assist in stripping leaves.
The