Andres --

Lucy is more than 300 million years old

Bipedal walks on 2 feet
Quadropedal walks on 4 feet
Natural Selection
There were animals between chimpanzees and us
Darwin didnt publish until Wallace did because he was afraid
Evolution does not produce the best
Evolution is the foundation of all life science
Ribo/Deioxiribo nucleic acid R/DNA
RNA world hypothesis
Garbag bag hypothesis: You need to have stuff to survive natural selection
Clay was the surface that made polymers out of monomers
Theory: life started around underwater vents smokers
Ingredients for life
1. Basic elements and organic compounds
2. Complex biomolecules
3. A membrane enclosure
4. Selection & evolutionary change
Stars make elements
When a star uses up H, it burns He, then C and the natural elements and finally Iron. It explodes and the
rest are made in the explosion
Many carbon-based molechles including CO2 and amino acid were brought to earth by asteroids
Earths oceans were a rich array of organic molecules
Our solar system formed 4.-4.6 billion years ago
The earth surface cooled sufficiently to have oceans by 4.0 b years
First fossil evidence of life is about 3.7-8 b
Stanley Miller setup experiment to mimic early earth. Found oranic compounds, amino acids, building
blocks for protein
H and other elements covalently bond with C to form
Carbohydrates are good sources of energy
Lipids: can be made into membranes
Proteins: building blocks
Nucleic Acids
RNA world hypothesis
Ancient Viruses use RNA as Genome not DNA. Some are still
common like influenza and hepatits
RNA acts as a catalyst
Only RNA initiates DNA replication
RNA regulates gene expression, repairs genes, carries genetic
information from DNA to ribosomes
Ribosomes are a machine out of protein and RNA and is essential for catalytic polypeptic activity
DNA needed to make protiens but protiens needed to make DNA.
Proteins known as enzmes catalyze reactions
Proteins were thought to the only biological molecules capable of catalysis
RNA is a molecule that makes itself
Natural bilayers are made of phospholipids with a hydrophilic head and 2 hyrdrophilic tails.
The cell membranes of cells are made of a lipid bilayer
Membranes sef-assemble

Emigrant properties: The sum is greater than its whole
Properties of NA CL
Solid, weight 23 gas, dimmer Cl2
Melting 98c, boiling 888c weight 35, Melting point -101 C
Amino acids are like legos because the can fit together easily
Emergence is a property of living and nonliving systems.
Emergance = order and self organization in non-living systems & living systems are similar
The Sum is greater than the whole
Both depend on energy flows
Emergence in simple systems may provide clues to how lifeless molecules led to living things
Find out about Emergent Complexity
# For order at any level to exist, order must have a root
#Order from metaphysical: very old idea
# Second law of thermodynamics: In Fact everything strives towards maximum entropy,
Self-organized phenomenon defy the Second Law of Thermodynamics which states that everything in
the universe becomes less ordered
Entropy is a measure of a systems degree of organization
In a system a process can only occur if it increases the total entropy of the universe. Energy
transformations involved in the processes are never 10% efficience. Some energy is always lost as heat
Higly ordered systems have low entropy
Disordered systems have high entropy
If a reaction is spontaneous due to large positive increase in entropy, its said to be entropy driven
Prtoein folding & formation of lipid bilayers are spontaneous and entropy driven
Let me give you an example other than my children
They are spontaneous processes.
# What about bringing these concepts to computer science and economics
Erwin Schrodinger wrote What is Life?
To maintain itself and escape inevitable dissolution demanded by the 2
nd
law, life constantly takes in
environment
Living matter evades decay to thermodynamic equilibrium by having a metabolism
S pore: Dehydrated life
You go to thermodynamic equilibrium when you die.

When talking about biology education Heres a fact heres a fact heres a fact. Who gives a shit!
I hadnt had children yet, I wouldnt go near his lab
I was not a good kid. I cant help it.

The Three major domains of the living world
Bacteria Archaea Eucaryotes
Bacteria and Archaea lumped together until Woes defined Achaea

All extant cells:
Enclosed by membrane:
Store hereditary information in DNA
DNA is much more stable
RNA molecules mutate faster

All extant cells: emc;psed by a membrane
Store hereditary information in DNA
Replicate there DNA using same basic mechanism
Use RNA for transcription of DNA.
RNA has planned obselescense.
Translate RNA into protein via tRNA & ribosomes
Use proteins as catalysts
Use ATP for free energy
ATP is made in chloroplasts

Prokariotes are single celled and not bacteria
No nucleus
Ribosomes are the factories that make protein

All most all bacteria have cell walls

Cell wall preforms osmosis to keep pressure correct

Sometimes bacteria have a greasy capsul
Bacteria in arid area have capsul which protect from dehydration
Bad bacteria with capsuls have advantage because white blood cells cant grab it
Ecoli is a colon bacteria

Dont hipe the wrong way
Learn the cell parts of Eukariotic cells and the kingdoms in the slides and plant and animal cells

The golgi bodies sends things in vesicles to thri right place.
Cytoskelatel elements and microtubuls are the highways
Mitochondria are the fuel pumps. They produce ATP
Triggering pathways in a cell can kill it.
Eukariotic cells are 10-100 times bigger than prokaryots. They are compartmentalizeds
Everything in an animal cell is in a plant cell.
Plants have chloroplasts which make ATP
Plant cells have vacuels to put waste in and maintain osmotic pressure.
There are 500 common cellular metabolic reactions with many interconnections
Most free living archaea in a Eubacteria have 1000-400 genes
Eucaryotes have more Gees and variety of Organelles mitochondria et.

Why do we have more genes than prokaryotic cells if we have so much in common.
We have many many more cells. Were more c complex. We have organelles with specific functions.
Archaea: Extremely s mall archea isolated from acid mine drainage in calfornia: Really small.
Live of reduction and oxidation of iron.
Extremophiles.
They had a non-oxygenic form of photosynthesis.
Organisms had heat sheilding using pigments which from photosynthesis evolved.
The biggest whipeout of organisms was when plants produced oxygen
Anaerobes dont use oxygen
Photosystem 1 is older and cyclicial
Chloroplasts have double layered membranes.
Chloroplasts are individual organisms within plasts in symbiotic relationship,
We need oxygen for ozone
First eukaryotes appeared in fossile record 2.8 BYA
Single cells are 50% of the living biomass.
Multicellularity allow division of labor and collaboration
First multicellular orgaisms are formed in Australia

Darwin
Erasmus Darwin: charles grandfather, physician, philosopher, poet
All of life comes from one animal
Simple changes over time
La marq:;
Aquired characteristics
Characteristics are acquired during life and passed down at birth
Natural laws
William paley:
Natural Theology, 1802
Pocket watch metaphor
Thomas Malthus
What applies to other animals applies to us
Recourse limitation
Phenotype= characteristic
Directional selection: Skews the population
Disruptive selection: Forms at both ends of range of variation. Intermediate are selected agains
If I dont know pick directional
Know Stabilizing Selecion and the others
TEST
Two short essays
Write relevant essays
Everything is fair game
Everything in evolution

Coevolution
When two species drive the others evolution
Predator pray relationship
Know alleles
NEXT TEST

Why do men compete and women choose?
Because they need to care for it.
Ornaments signal good alleles
Male seahorses carry babies
Behavioural difference between monogamous voles and polygamous
The human signal of good alleles
Voles have a monogamous gene
There are multiple versions of the monogamy and it is found in humans in 17 different lengths (alleles).
The gene involves vasopressin which does homeostatic regulation of salt in the blood. Homeostasis
A-Vessopressin has more arginine and doesnt interact in blood. It goes to brain and has a receptor in
the brain. It is linked to social and sexual behaviors. Triggered during aftersex. If the receptor has the
short gene length it is the happiness receptor.
Genetic drift is a phenomenon that can occur randomly
Genetic drift is easier to fix in large populations
Heterozygous: One allele for each characteristic
As heterozygosity decreases, genetic flexibility is lost like in in-breeding
Cheetahs have low heterzygousity
Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population due
to random sampling.
[1]
The alleles in the offspring are a sample of those in the parents, and chance has a
role in determining whether a given individual survives and reproduces. A population's allele frequency
is the fraction of the copies of one gene that share a particular form.
[2]
Genetic drift may cause gene
variants to disappear completely and thereby reduce genetic variation.
Cheetah population = 1000
Bottleneck effect
Deleterious alleles become homozygous
There are fewer, less viable offspring.,
Adaptive radiation
Species are groups of interbreeding natural populations that are reproductively isolated from other
groups Ernest Mayr
How do you achieve reproductive isolation pre-coming to Rensselear
Pre-zygotic and post-zygotic
Specieation is the attainment of reproductive isolation
Application of BSC to many groups problematic because of hybridization between clearly deliminated
species
BSC doesnt apply & hence of of no help in deliminating species in asexual populations. (e.g. self
pollinators)
If ribosomal RNA it is likely you are same species
In practice BSC cant be applied to delimit species.
Insects have the largest nomber of species
10-100 million species on earth
Only ten phyla are terrestrial
Insects can make up 40% biomass
300 000 beetle species

Grand canyon
North rim Kaibab squirrel
Sout Rim Aberts squirrel
Ancestral population devided by canyon
Barriers
Mountains
Rivers
Glaciers
Islands
Land (especially freshwater)
water
glaciers prevented homos from interacting
parapatric speciation:
Adjecent populations evolve into distinct
Maintain contact

Larvae moved from hawthorne to aples
Chemical sensing altered by muttion
Second mutation enhanced larval survival depends on apples
Genes promoting earlier emergence also selected for

Blue indigobird lays eggs in nest of African firefinch & black-bellied firefinch
Baby indigo birds learn songs of their respective foster finches and have developed two races
Females prefer males who know same finch song
Leading to speciation
On average species last 4 million years
65 million 5 mile wide asteroid killed dinos
Know adaptive radiation
6 mass extinctions in last 600 million years

Iridium layer caused by asteroid

3 models for recovery

1. Starts Immediately
2. Recovery lag time ~10my
When all living systems need energy they use ATP
Amino acids build all protiens
There are L and D forms
Only L forms are used to make protiens
Nothing above the level of a virus uses anything but DNA for genetic material
Viruses can use RNA and DNA
Virtually all catalysis occurs because of protein activity
Mitosis goes with eukaryotic cell division only
Miosis occurs with euks when making gamytes only
Prokaryotes use cell division
Humans have 60% dna with fruit fly diverged 300 million years
60% with chicken 200 MYA
99% similar with chimps diverged 6 MYA
Bananas 50% 1 BYA
Aerobic organisms conserve
Superoxide dismutase cleans up free radicals
Hydrogen peroxide???

Breading of animals:
Dogs Canis Familiaris
There are about 5 gene differences between dogs
It is physically possible for dogs to mate with wolves

Kettlewells experiment: moths were released
Moths turned dark brown in industrial cities and white in country
Criticisms
Released too many moths
To few release sites
Moths released onto tree trunks, usually rests under branches
Mixed wild and lab bred
Judith hooper said moth thing was hoax
Michael majerus avoided mistakes and came up with same results

Human Evolution
Austrolopithicus is ape like
Homo Erectus Sapien

Oldust primate = Ignatius clarkorkensis
About size of mouse
From wyoming
Most primates were arboreal (tree) and ate fruit
Will be a question on Anthropods, hominoids and hominids tree, dont need to draw tree,
need to know difference
Our lineage is controversial and full of dead ends

Ida
Bridges evolutionary split between higher primates & humans
First link to hall humans
Only complete fossil primate of any age
Aegyptopithecus Zeuxis
Discovered in 2006 in Egypt
30 mya
Arboreal, fruit eating
Size of housecat
Tiny brain
Order primates
Other primates still live in trees and eat fruit juice
Tropical

The most important trait developed in the evolution of primates is the grasping hand. It is how we
manipulate the environment around us to fulfill our needs. Most mammals have some form of parental
care, sociality, and binocular vision. A big brain might not even evolve unless grasping hands existed
previously, for a big brain would serve little purpose if it could not be used to skillfully interact with the
world. Grasping hands is what allowed monkeys to grip branches. Using tools is a defining characteristic
of humanity and it depends on the versatile hand.
During the myocene: Africa was covered with trees and full of apes
Human foot is great and preserved in litoly footprint
Dr.richard Leaky is an evolutionary researcher who studies bipedalism
Brain size is linked with body size


Humans brain size 3x lucy
On islands species get smaller
Chimpanzees can catch bugs, use tools, and hunt in parties
Neanderthals were very successful during ice age Europe. They were isolated
Neanderthals may have blended with humans
Maybe the conflicted with homo sapiens
Causal relationship between Neanderthals and humans
Neanderthals
DNA is distinct from modern humans
Wore clothing
Buried dead
like us
Successful for long time
Skeletal and cranial differences
Probably language capabilities
Cared for others
had art, jewelry
Made a flute
Hyoid bone is not connected to other bone
Out of Africa Theory
branched in Africa and wen to other parts of world.
Divergence 600-800 thousand years ago based on DNA
You have mothers mitochondria
Small hominid, homo fluersiences, The Hobbit, 3 feet tall 18,000 years ago in Indonesia
Stature and wristbone are different
Out of time
We think homo erectus is our direct line
Artipithicus ramidus 4 feed, 4.3 mya
Somewhere between biped and quadroped
We know homo erectus spread first
Why isnt there speciation in humans? There wasnt enough gene flow for people to stay thee same
Out of Africa: Arose in one place and stayed there a long time
Arose in sub Saharan Africa
Moved into areas Erectus preceded them
Only leaving Africa did phenotypic differences arrive
Other theory: 180,000 years old and originated only in Africa, explains old fossils
Young species are genetically homogeneous
Climate changes allowed us to move into Europe
Africa Cradle of human evolution
No human fossils older than 2 mya exist except Africa
Homo Erectus left Africa in waves
Regional Model holds that we evolved in multiple regions
Mitochondrial DNA used to determine evolutionary history from mtDNA of todays human population
Mutates 10x faster
Inherited from mother
Has 37 genes
Mostly independent fro mrest of cell
Screwed up mitochondria get eaten by lysomes
Africa has the most genetic variationshg
Dawn of art 33,000, Venus
Flutes: 45,000
100,000 Necklaces
Religion 35
War and Violence
Cooperation and Altruism
Pairbonding
Why might have these universal behaviors have evolved?
War is a way for a nation to compete with other nations for recourses. Because the stronger one wins,
the winning nation reproduces more than the losing nation, leading to a stronger species. It is also a way
for societies to remove weaker males. Fewer men than women are necessary for a society to reproduce,
and because wars are mostly fought by men, it is a way for societies to allow only stronger males to
reproduce. The pressure of war also drives government to develop new technology that is later used
during peacetime.
Chimpanzees hang out in troops with 39 distinct behaviors
Chimps make tools.
They hunt in teams
John Locke David Hume John Jacques Rousseau Ed Wilson
Tabula Rasa Innate ability Humans are good but corrupted by society Nature & Nurture
3 Genes create stuttering
Watch Holistic vs. Reductionist View Video

Cancer happens in mitosis
Cancer is mutations in the normal process of mitosis
Karyotype of pancreatic cancer cells
What do you notice that appears odd amongst these chromosomes.
Cells split by mitosis
Wound healing works by mitosis.
Humans have 100 trillion cells
Millions of cells divide e very second
Rate of division depends of cellskin cells divide once per hour
Differentiated muscle and nerve do not divide
Cytoconesis: division of cell into two
When done with mitosis & cytokinesis, each chromatid has 1 chromosome and chromosome gets
duplicated
These chromosomes are stuck together by cohesions
There are phases that make sure things are going well doing division
Cells do nothing else during mitosis
Know the names of the cycle what they do.
How chromosomes move to opposite sides
How they hookup
What happens to nuclear membrane?
Microtubulis are the highway
Chromosomal abnormalities associated with cancer
Mitosis disorder
1 in 8 women will face breast cancer
When cancer becomes metastatic it goes to rest of body
Radiation therapy kills all cells
Taxol is extracted from a tree
Freezes mitotic spindle in actively dividing cells
Phases of cell division
G1 S G2 M
Sister cells have same DNA have twin chromatids
Cells have controls
Quiz on cell cycle
Gregor Mendel
Pea plants
Ran an abbey
Tested 29k pea plants
Published 1860s
Recognized in 1920s
Meiosis
Haploid gametes
22 autosomal chromosmes
1 sex chromosome
Meiosis adds variability of alleles

In the beginning, the chromosomes dont end up exactly as they started,.
Haploid cells mature into gametes
The more recombination the greater diversity
Homologous chromosomes carry different versions of the genes
Know mendels two laws
Mendel discovered the fundementals of genetics
Invented quantitative approach for the study of inheritance
1. Heritable factors (genes) retain their individuality and do not blend
Mendels law of Segregation
1. There are alternatives versions of a trait (alleles)
2. If two alleles of an inherited pai differ, one can determine the appearance.
3. Each individual has two allels of a gene
4. Each parent contributes one of two alleles
Know qustoins of mendelian inheritance and genetics
Two different genotypes can result in same phenotype
Law of segregation
Gene on X chromosome is not mendelian
Mendel disproved dominance theory

SRY gene is on Y chromosome is one of 307 genes on Y Master for male sex determination.
Male and femaleness can very depending on which genes and receptors are activated.
Chromosomes alone are not sufficient
Neddy steven discovered chromosomes
Carbohydrate chain are on the surface of red blood cells which the immune system uses to
distinguid
Type O has no carbohydrate
Codominance when two allels of same gene are expressed
Sicle cell anemia. One amino acid is witched from one to another
People show symptoms of cicle cell under oxygen deprivation
Malaria occurs in areas of high homo/hetero? zygosity and sickle cell

Spectral karyotyping: A Diagnostic tool.
SKY
Fluorescent dyes interact with regions of chromosome
Reveal abnormalities
Philidelpha chromosome:
White blood cell cancer
Too many white bloodcells
Approximately half of fetuses spontaneously aborted in first trimester have chromosomal
abnormalities.
Grils are less likely to have fragile X because they have two
Humans cant handle tetraploid and anything but diploid is bad
Down Syndrome
1 in 800
Most common chromosomal disorder
Down syndrome is a spectrum disorder
Chromosome 21
Before a woman is born they have a maximum number of O sites so they get old. Theyre
stopped in miosis 1
If a women is too old they get a nondisjunction in meiosis II and get down syndrome
Amneose senticis is risky.
Female Chromosomal disjunction
XO
Turner syndrome XO
1/2500 females
Social disorder
Male
Klinefelter syndrome XXY
Normal range of intelligence, low sperm count, learning disabilities with language
XYY
1/500 1/1000 males
Taller and usually fertile
TEST
Genes and medicine 1-4
5-9 next test
DNA is double stranded
RNA is single stranded
Purines: Adenine & Guanine
Pyrimidines: Cytosine, thymine, and uracil
RNA have ribose
DNA has dioxiribose
Have to memorize: Purines, Pyrimidines
Uracil and thyrine substitute for eachother and dont occure together
RNA does everything
DNA C-G, A-t, T-A are hydrogen bonds that always occur together
The people who discovered the structure of DNA were based off work of Rosalyn franklin and others
DNA have a little phosphate and sugar

Chargas Rule
The amount of A and T and C and G are equally proportionate
Rosalyn Franklin died or she would have won the nobel prize.
The Watson and Crick report was 1 page long.
They borrowed her data without showing her

Question
Can you suggest a way for one copy of the DNA to make two?
One double helix might split into two. Provided with enough ATGC, the ATGC would attach to their
pairs forming hydrogen bonds. Around each strand of the DNA, another one would form with the
matching sequence of ATGC.
We should know the DNA enzymes on Animation of DNA replication slide
It unwinds at the speed of a jet eningine
One side is made continuously and another is made discontinuously
Ligase is an enzyme that fixes DNA
DNA is flexible about its long axis and can be bent
There is an equal weight basis of DNA and histome
Chromosomes are condensed in M phase
Genes are units of heredity
RUBISCO most abundant protein on earth, in plants
Polymorphism: Differences in DNA
Each transposons have resulted from a jump
Watch videos
Clusters
Family
Olefactory superfamily
Genes have junk between them
DNA is 1.5% Exons
Genes and Medicne 1234 not 5
Test Tuesday
Introns are genes that interrupt and are the sensible part of the gene
Venter developed DNA sequencing business
DNA need primer
Most video stuff is not on test
They started sequencing genomes with influenza
End of exam material
How DNA Becomes protiens
Transcription converts DNA to RNA. THE RMA goes to the RNA which gets translated to ribosome
Ribosome makes amino acids which make polypeptide. Proteins are made in cytoplasm
mRNA = Message RNA
Strands of DNA are Watson and Crick

THIS IS ON NEXT TEST
Attendance Exercise
What would happen if you copied both strands of the Gene
RNA and DNA are anti-parrallell
Multiple amino acids can mean same thing

The enzymes only know how to go one way so it will have to copy one strand of DNA from the other
end. When copying from the end there would not be information.