A Brief History of Biology

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A Brief History of Biology
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Black Boxes Within Black BoxesorWheels 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 didnt advance until the
  17th and 18th centuries

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• 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

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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

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The Inner Life of A Cell

• http//multimedia.mcb.harvard.edu/ (narrated)
• http//aimediaserver.com/studiodaily/videoplayer/?
  srcharvard/harvard.swfwidth640height520
  (unnarrated)

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Classification
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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

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• 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)
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• 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

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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)
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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
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Homologies
A homology is a character shared between species
that was also present in their common ancestor
the more homologies, the more closely related
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Problems with homologies Convergence species
from different evolutionary branches may come to
resemble each other if they live in similar
environments
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Analogies anatomical features that have the
same form or function in different species that
have no known common ancestor
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Classification

• The Pneumonic
• King Philip Came Over For Good Sex

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Shark
Dolphin
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Evolution
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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.

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Darwins 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

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Darwins 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 Lyells 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.

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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
  dont say species cant 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.
• Lamarcks theory of Evolution (1802) Using or
  not using body parts leads to inheritance of
  those parts

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Two Theories of Note

• CATASTROPHISM

• GRADUALISM

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

• 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.
• Darwins thinking about species formation was
  essentially gradualism in biology.

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Changes in Thinking

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

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Luis Alvarez Impact Event Hypothesis

• It 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.

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The Current Theory of Lunar Formation

• Currently, the only viable explanation of the
  presence of earths 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.

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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

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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

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Homologous Structures

• Features with different functions but structural
  similarity due to common ancestry

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Analogous Features

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

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Comparative Embryology

• Closely related organisms often have similar
  stages in embryonic development

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Molecular Biology

• The universality of genetic code allows species
  to be compared on a molecular basis

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Hemoglobin Comparisons

• This 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.

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The Darwinian Mechanism Natural Selection
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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

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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 populations DNA.
• Microevolution The change in the frequency of
  alleles in a populations gene pool.
• Macroevolution That change of one species into
  another.

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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.
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Micro EvolutionSpecies Change over Time
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Microevolution

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

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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

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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 thats 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

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Hardy Weinberg Equilibrium

• 5 conditions must be met to keep a gene pool
  constant
• A Large Population
• The Population is Isolated
• Mutations do not alter the Gene Pool
• Mating is Random
• All individuals are Equal in Reproductive Success

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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)

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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.

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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 its 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

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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 hes 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

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The Observable Outcomes of Natural Selection
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Stabilizing Selection

• What usually occurs in stable populations. The
  extremes are culled.
• Example Brown Trees and Brown moths.

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Directional Selection

• Eliminates individuals at one of the extremes.
  Occurs during periods of environmental change.
• Example Taller trees and giraffe necks.

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Divergent Selection

• Extreme individuals are favored.
• Example Short billed ducks and long billed ducks.

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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

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Darwins 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.

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Selection Cannot Fashion Perfect Organisms

• Historical Constraints
• Evolution cannot scrap ancestral forms
• Features can be modified only slowly
• Adaptations are Compromises
• Features usually have several functions as an
  organism must do several different things to
  survive
• Not all Evolution is Adaptive
• Chance is the governing role in mutation and
  species adapted to a particular region are often
  relocated to random ones
• Selection only Edits
• Only the fittest phenotypes are selected, which
  may not be ideal ones.

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Macro EvolutionParticles to People
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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

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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

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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

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Punctuated Equilibrium

• The idea was put forth in 1972 to describe gaps
  in the fossil record

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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

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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

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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

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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

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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

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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

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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