A Brief History of Biology

Black Boxes Within Black Boxes

orWheels within Wheels

The Age of Naked Eye Investigation

• Around 400 BC certain texts attributed to Hippocrates described certain ailments and attributed them to diet and other physiological causes

• Living matter believed to be made of four humors: blood, yellow bile, black bile, and phlegm

• Aristotle investigated nature in a systemized manner, developing categories for life (many of which are still used)

• Galen, a Roman physician (200 AD), attempts to understand life through dissection. He determined that the heart pumped blood, but not that it circulated (this was only discovered in the 17th century by an Englishman, William Harvey.

• Biology, essentially didn’t advance until the 17th and 18th centuries

The Age of the Microscope• Galileo uses a microscope to observe the compound

eye of insects• Several others followed observing capillary blood flow,

micro organisms, cells in cork and leaves, etc.• Early 19th century: The Cellular Theory of Life was

proposed by Schleiden and Schwann: that all life was based on cells and cellular secretions, also that cells have a life of their own despite their part in larger organisms

• Cells looked very simple at this time and its function was assumed to be simple

• It was discovered, by Wohler in 1828, that living matter is made of the same fundamental stuff as non living matter

Limits to the Microscope• For physical reasons a microscope cannot resolve two points closer

together than ½ the wavelength of light• Most structures in cells are too small to be seen with these

microscopes and eluded discovery• After WWII the electron microscope was developed and the cellular

world was found to be more complex than ever imagined• The ultimate function lay beyond even what could be seen with the

electron. Life is based on Molecular Machines• Proteins, the building blocks and building machines, of life were

modeled… and found to be incredibly complex– “Could the search for ultimate truth really have revealed so hideous

and visceral-looking an object?” – Max Perutz 1958• DNA, not protein, is discovered to be the blue print for life

The Inner Life of A Cell

http://multimedia.mcb.harvard.edu/ (narrated)

http://aimediaserver.com/studiodaily/videoplayer/?src=harvard/harvard.swf&width=640&height=520

(unnarrated)

Classification

Taxonomy and Phylogeny – lending order to investigation• Species (from the Latin: kind): A group whose

members posses similar anatomical characteristics and have the ability to interbreed.

• Speciation: The evolution of a new species• Taxonomy: The branch of science concerned

with naming and classifying the diverse forms of life.

• Phylogeny: the sequence of events involved in the evolutionary development of a species or taxonomic group of organisms

• Linnean System – Binomial Nomenclature

How many species are there?

- about 1.8 million species have been given scientific names

- nearly 2/3 are insects

- estimates of the total number of living species generally range from 10 to 100 million (most are insects and microbes)

Linnaean system of classification

-used in the biological sciences to describe and categorize all living things

- Taxonomy - classification of organisms into different categories based on their physical characteristics; used before genetic testing

The Linnaean system uses two Latin name categories (genus and species) to designate each type of organism

- genus: higher level category that includes one or more species under it

Referred to as binomial nomenclature

Ex: Humans are (genus) Homo (species) sapiens (“man who is wise”)

Biologists classify organisms into different categories by judging degrees of similarity and difference that they can see

- the assumption is that the greater the degree of physical similarity, the closer the biological relationship

Homologies

A homology is a character shared between species that was also present in their common ancestor; the more homologies, the more closely related

Problems with homologies

Convergence: species from different evolutionary branches may come to resemble each other if they live in similar environments

Analogies: anatomical features that have the same form or function in different species that have no known common ancestor

Classification

• The Pneumonic– King Philip Came

Over For Good Sex

Kingdom: Animalia

Phylum: Chordata

Subphylum: Vertebrata

Class: Chondrichthyes

Kingdom: Animalia

Phylum: Chordata

Subphylum: Vertebrata

Class: Mammalia

Shark Dolphin

Evolution

Introduction: Charles Darwin 1809 - 1882

• He studied medicine at Edinburgh University• Then theology at Cambridge• During his five-year voyage on the Beagle he

established himself as a geologist• He published journals of the voyage, making

him a popular author• He was intrigues with species diversity and

conceived his theory of natural selection in 1838

• In 1858 Alfred Wallace sent him an essay describing his idea, which prompted a joint publication

• In 1859 he published: On the Origin of Species

• Since that time evolution from common descent has been accepted as the dominant explanation of diversity in nature.

• Though reticent about his religious views, in 1879 he responded that he had never been an atheist in the sense of denying the existence of a God, and that generally “an Agnostic would be the more correct description of my state of mind.”

Darwin’s Ideas

• The Observation– That species change over time

• The Implication– Perhaps all living species arose from earlier forms

• What he knew nothing about– Genetics–Mechanisms of Inheritance

• What he never saw in his life– Irrefutable proof

Darwin’s Evidences

• He noted that South American fossils were more similar to present day South American species than to the species of other continents.

• He read Charles Lyell’s work, Principles of Geology, and was introduced to Gradualism.

• Noted how species on the Galapagos Islands are unlike those anywhere else.

• He hoped to find extensive evidence of this in the fossil record.

Is this a New Idea?• Anaxiamander (500 BC) believed life arose from water and that simpler

forms of life preceded more complex ones• However, Aristotle taught that species were unchanging. His logical

conclusions dominated the theological thinking of the three great Western Patriarchal religions: Judaism, Islam, and Christianity.– An aside: The Holy Scriptures of these religions don’t say species can’t

change, rather the men interpreting those scriptures said it.• In the 1700s fossil studies began to suggest that the earth was older than

6000 years– An aside: The Holy Books describe creation occurring in segments described

as days, which could be of any length of time since the sun was not made until the 3rd.

• French naturalist, Georges Buffon, suggested that these fossils may be earlier forms of current species.

• Lamarck’s theory of Evolution (1802): Using or not using body parts leads to inheritance of those parts

Two Theories of Note

CATASTROPHISM

• The idea that Earth has been affected in the distant past by sudden, short-lived, violent events that were sometimes worldwide in scope

GRADUALISM• From 1850 to 1980 scientists

rejected catastrophism• Instead they believed that the

earth had been shaped by the long term action of forces such as volcanism, earthquakes, erosion, and sedimentation, that could still be observed in action today.

• Darwin’s thinking about species formation was essentially gradualism in biology.

Changes in Thinking

• Catastrophism reevaluated in the 1980s due to new discoveries and the implications of modeling systems.

Luis Alvarez Impact Event HypothesisIt is believed that a 10km asteroid struck the earth 65 million years ago and ended 70% of all species of the Cretaceous period, including dinosaurs.

The Current Theory of Lunar FormationCurrently, the only viable explanation of the presence of earth’s massive moon is the near miss of a Mars sized planetesimal 4.5 billion years ago. The resulting debris formed an accretion disk which the moon formed from.

Evidences of Evolution

The Fossil Record

• Currently considered the best evidence of species evolution

• It demonstrates a historic sequence in the appearance of species– Less complicated life forms predate more complicated ones– The oldest fossils are prokaryotes (bacteria), dated 3.5

billion years– Fish are the oldest vertebrates

• Despite this order, transitional species are almost completely absent in the fossil record

Other Evidences • Biogeology – The similarity and specificity of organisms in isolated

regions• Comparative Anatomy – Body structures in different species.

Anatomical similarities among many species indicate common descent. – Homologous Structures: Features with different functions but structural

similarity due to common ancestry – Analogous Structures: Features with structural similarity due to similar

environmental pressures yet the species in question have no ancestral relation

• Comparative Embryology – Closely related organisms often have similar stages in embryonic development

• Molecular Biology – The universality of genetic code allows species to be compared on a molecular basis. – Hemoglobin Comparisons

Homologous StructuresFeatures with different functions but structural similarity due to common ancestry

Analogous FeaturesFeatures with structural similarity due to similar environmental pressures yet the species in question have no ancestral relation

Comparative EmbryologyClosely related organisms often have similar stages in embryonic development

Molecular BiologyThe universality of genetic code allows species to be compared on a molecular basis

Hemoglobin ComparisonsThis complicated protein is used in many species to carry oxygen molecules. The sequence of amino acids (the building blocks of proteins) varies more the father separated species are.

The Darwinian Mechanism: Natural Selection

Natural Selection

Organisms are in competition due to environmental pressures and limited resources

• Natural Selection – The fittest will breed most• Artificial Selection – Human manipulated

selective breeding– Domesticated animals– Domesticated plants

• Example: Insect resistance to pesticides• Example: Bacterial resistance to antibiotics

Definitions

• Population: A group of individuals from the same species, living in the same space, at the same time.

• Species: A population of individuals with the ability to interbreed and produce fertile offspring.

• Gene Pool: The sum total of a population’s DNA.• Microevolution: The change in the frequency of

alleles in a population’s gene pool.• Macroevolution: That change of one species into

another.

Evolutionary Trees

Using either physical features or molecular analysis species can be classified into branching family relations. In essence, this is a hierarchy of complexity.

Micro EvolutionSpecies Change over Time

Microevolution

•Species change over time•These changes may occur naturally or they may be induced by human interaction

Non Evolving Populations

The Gene Pool of non Evolving populations remains constant

• Sexual reproduction alone does not lead to microevolution; it merely shuffles the genes

• Gene Pool: all of the various genes in any member of a species anywhere

An Example• Humans have two copies of almost

every gene (23 chromosomes from each parent)

• Let us imagine genes to be cards, each card representing a certain trait

• The cards come from the card pool• As long as the cards say the same

thing I am not evolving• For example, you get two cards for

eye color, but there are more than two eye colours out there

• A human genome contains only about 30,000 genes; though that number is being debated

• We get a huge variety of hands, but that’s just the luck of the draw

• For microevolution to occur something must change a card itself or cause a certain card to appear more or less frequently

Hardy Weinberg Equilibrium

5 conditions must be met to keep a gene pool constant

1.A Large Population

2.The Population is Isolated

3.Mutations do not alter the Gene Pool

4.Mating is Random

5.All individuals are Equal in Reproductive Success

Causes of Microevolution

• Genetic Drift: A completely random process. Any small portion of a population may not represent allele frequencies well– Example: Coin Tosses– Bottleneck Effect: Drift caused by an event, which

drastically reduces population size. Catastrophe or colonization can cause this.

– Founder Effect: A small group of colonizers which breed largely with themselves (Amish, European Nobles)

– Gene Flow: Fertile individuals moving in and out of populations. It reduces genetic differences. (Spain and Southern Italy)

Causes of Microevolution

• Natural Selection: The only process which allows adaptive change in a species. – Question: Do beneficial genetic advantages always

lead to improved breeding?• Mutation: The ultimate source of new genetic

information. – With the previous two we have only changed the

frequencies of the “cards.” – This mutation must produce a new allele. – Natural mutations occur in DNA sequences once in

100,000 to 1,000,000.

Variation and Natural Selection

• Not all variation in populations is inheritable• Polygenetic Inheritance: When multiple genes affect one trait

– Hair color• The offspring of species vary due to two processes: Gene shuffling

and mutation– Both processes are completely random– Selection only affects a gene if it’s manifested, ergo recessive traits

cannot be influenced by natural selection– Mutation is almost always harmful

• When a mutation leads to improved breeding this gene will become more common in the species.– Bacterial resistance

• Endangered species suffer from a lack of genetic diversity– Cheetahs and Bananas

Survival of the Fittest?

• Direct competition between members of a species for reproductive privileges is relatively rare

• Survival alone does not guarantee reproductive success– The biggest, toughest, fastest frog in the pond has a

fitness of zero if he’s sterile• Darwinian Fitness: The contribution an individual

makes to the gene pool of the next generation relative to the contribution of other individuals– Implication: The fittest individuals are those who pass

on the greatest number of genes to the next generation

The Observable Outcomes of Natural Selection

Stabilizing SelectionWhat usually occurs in stable populations. The extremes are culled.

Example: Brown Trees and Brown moths.

Directional SelectionEliminates individuals at one of the extremes. Occurs during periods of environmental change.

Example: Taller trees and giraffe necks.

Divergent SelectionExtreme individuals are favored.

Example: Short billed ducks and long billed ducks.

Sexual Dimorphism

• The secondary sexual characteristics between males and females– Size– Color– Behavior– Adornment

• Generally, males are the showier sex in nature and use appearance or behavior to attract females

Darwin’s Concern

• Fascinatingly, showy plumage and adornment offers no survival advantage and would be reinforced only by choice.

• In these instances successful breeders are less fit for their environments

• Since we preserve the weakest of our species, Darwin was concerned that we have effectively halted beneficial evolution.

Selection Cannot Fashion Perfect Organisms

1. Historical Constraints– Evolution cannot scrap ancestral forms– Features can be modified only slowly

2. Adaptations are Compromises– Features usually have several functions as an organism must do

several different things to survive3. Not all Evolution is Adaptive– Chance is the governing role in mutation and species adapted

to a particular region are often relocated to random ones4. Selection only Edits– Only the fittest phenotypes are selected, which may not be

ideal ones.

Macro EvolutionParticles to People

Macro Evolution

• It is proposed that microevolutionary changes will induce speciation events given sufficient time

• It is assumed that all organic life is descended from one simple life form

• Speciation events are not generally observable– The London Mosquitoes

Darwinian Evolution Modified

• Darwin believed that species evolve steadily, slowly, and predictably

• Due to that he predicted seeing a steadily changing fossil record

• This was not found, rather we see distinct species

• Occasionally we see massive destructive periods where large numbers of species are wiped out, in the aftermath we see many new species arriving

Revising ThingsPunctuated Equilibrium

• In the past 50 years, some evolutionary biologists, frustrated by the lack of transitional forms, developed a new hypothesis

• The hypothesis is known as punctuated equilibrium and describes evolution moving in spurts, with new species diverging abruptly

• The other theory about the gaps in fossil records is that the intermediate species in question migrated, thus eluding fossil detection in that region

Punctuated EquilibriumThe idea was put forth in 1972 to describe gaps in the fossil record

The Molecular Question

• In the past 20 years we have gained considerable understanding about several cellular processes and machines on a molecular level

• Cells are profoundly complex and mechanistic• Models for the generation of simple cellular machinery

from preexisting material are under debate• Pathways are suggested, but none have been accepted• This is a region of current research• Previously, arguments focused on anatomical

similarities

Simple to Complex Eyes

• It has been argued that human eyes are irreducibly complex

• It is clear from anatomical investigations that there are many simpler eyes than human eyes

• Human eyes, then, may be the most current in a series of anatomical jumps

The Molecular Question

• Even the simplest eyes rely on the same complicated molecular process• Where did this process come from?• There are no simpler forms of light detection• Currently there are no models of step wise evolution to a photo receptor

The Miller Experiment• Conducted in 1952 by Stanley

Miller• An investigation of the ability

of simple molecules to organize into amino acids, the building blocks of protein

• Early earth gasses were placed in a flask and subjected to electric shock resulting in the amino acids

• The early atmosphere is presently debated, nitrates will destroy amino acids as will O2

• Even with amino acids, they must be in correct sequences to do anything, and in a membrane

Suggestions on the Origin of Simple Cells

• We need data storage and replication for life

• That means RNA or DNA• Present cells process information:

– DNA to RNA to Protein• Certain RNA sequences can self

replicate without proteins• Some lipids spontaneously form

spheres• Perhaps RNA entered on of these

spheres in the right configuration to induce replication

• These amalgamations of cooperating molecular materials are called Co-ops

The Geological Timeline• In Geology it is assumed that appearance in time is related

to position in rock strata• There is a sequence to the appearance of life forms• Generally, simple organisms predate more complex ones• It is proposed that all forms of life now existent come from

a single precursor • Geologists have assembled time table describing these

trends• Radiometric Dating is used to estimate the ages of fossils• The half life of 14C is about 5,730 years, therefore that is the

limit of our resolution

Continental Drift

• Anciently the continents were together

• This was called, Pangea

• Slowly, they are drifting apart; about 2cm per year

• Species trapped on these continents have been evolving separately