Download Exam 1 set 2 Darwin Genetics

Darwin s Two Main Contributions
•  Carried out the necessary
research to conclusively
document that evolution has
occurred
•  Discovered the process by
which complex, functional
design originates in living
things: natural selection
Charles Darwin (1809-1882)
Darwin s Life
•  Family
–  English
–  moderately wealthy (mom was a
Wedgewood)
–  Dad influenced his career options
•  Education
–  Started in medicine at 16
–  Switched to theology at Cambridge
–  Interested in the scientific ideas of
geologist Adam Sedgwick and
naturalist John Henslow
–  At first, didn t believe evolution
occurred
–  Far more interested in biology than
theology when he graduated
The Beagle
•  Five-year voyage on the
H.M.S. Beagle (1831-1836) at
age 22 with Captain Robert
Fitzroy
•  Galapagos Islands
Darwin s Influences
Charles Lyell (1797-1875):
geologist who popularized
uniformitarianism (vs.
catastrophism
Darwin s Influences
Thomas Malthus (1766-1834) was an
economist who observed that more
individuals are born than survive to
reproduce; individuals are thus in a struggle
for existence, that is, competition
So, some individuals will reproduce, and others will
not. Question: are winners a random selection, or
do some individuals have an advantage over
others?
"The elephant is reckoned the slowest breeder of
all known animals, and I have taken some pains to
estimate its probable minimum rate of natural
increase; it will be safest to assume that it begins
breeding when 30 years old and goes on breeding
until 90 years old; if this be so, after a period from
740 to 750 years there would be nearly 19 million
elephants descended from this first pair.” (Darwin)
Darwin s Influences
•  One pair of mice is
capable of producing a
litter of six offspring as
many as six times a
year. Within six weeks,
each offspring can
produce litters of their
own.
Darwin s Influences
Artificial
Selection
Darwin
s
Influences
Comparative Anatomy
Vertebrate forelimb
Darwin s Influences
Fossils
Darwin s Influences
Geographic distribution of traits: beaks were well-adapted to
local environments on the islands
Adaptive Radiation in Galapagos Finches
Adaptive Radiation
Darwin s Influences
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Geology (Lyell)
Within-species competition (Malthus)
Artificial selection (breeders)
Comparative anatomy
Paleontology (fossils)
Geographic distribution of traits (finches)
...Natural Selection
Darwin s Short Definition
“I have called this
principle, by which each
slight variation [in a trait], if
useful, is preserved, by
the term Natural Selection.”
- From The Origin of Species
Natural Selection
•  Assumption 1: Reproducing entities exist.
•  Assumption 2: Variations exist, and they can be
passed on to offspring (heritable variation).
•  Assumption 3: Variations have reproductive
consequences.
•  Result: over time, the entire population will come
to possess the reproductively superior variation—
adaptations.
•  One example: camoflauge
Natural Selection, Redux
Reproducing entities exist.
Natural Selection
Variations exist, and they can be passed on to
offspring (heritable variation).
Natural Selection
Variations have reproductive
consequences.
Natural Selection
Over time, the entire population will come to possess
the reproductively advantageous variation.
Natural Selection
After thousands of generations…adaptations
Adaptation here: camouflage
Natural Selection
• Natural selection is the process by which favorable
traits that are heritable become more common in
successive generations of a population of
reproducing organisms, and unfavorable traits that
are heritable become less common.
• Over time, this process can result in adaptations
that specialize organisms for particular ecological
niches and may eventually result in the emergence
of new species.
Film: Evolution
•  On DVD in class
Darwin s Influences
Why did he wait so long to publish his theory of natural selection?
Alfred Russel Wallace
(1823-1913)
Example: Finches at Daphne Major
Darwin s Biggest Scientific Problem
• Darwin realized that
natural selection for
specific traits could lead
to changes in species
through time.
• However, Darwin lacked
information on how these
traits were passed from
generation to generation.
Genetics
Mendel was the first
to explore the units of
inheritance: genes.
Gregor Mendel (1822-1884)
What do GENES do?
They control the production
specific PROTEINS in living
things…
By stringing up small amino acid
molecules into long protein
strands…
Genetics and Protein
Synthesis;
Bodies are made of protein
and other stuff…
Organisms Components
•  Organism = a living thing
•  Generally all can be sorted into 5 (or 6)
kingdoms: animals, plants, fungi, bacteria,
protists
•  Made of molecules…
–  Protein: the stuff living things are made of, e.g., collagen,
enzymes, etc.); Also made of: water, carbohydrates, fats,
vitamins/minerals, DNA (nucleic acids), etc.
–  Proteins are long molecules that are folded over on
themselves
–  The components of protein molecules are smaller molecules
called amino acids (AAs)
Amino Acids
•  There are 20 kinds of AAs
that make up all the proteins
that organisms have
–  Such as: alanine, asparagine, methionine…
– Made of Hydrogen,
Oxygen, Nitrogen,
Carbon, (HONC) and
Sulfur (S only in
methionine and cysteine)
Amino Acids
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AAs are small molecules, but when strung up and folded over on
themselves to form a protein, they can be quite large
AAs are attached by peptide bonds
Amino acid strand
Each AA is like a bead on a necklace; electrochemical interactions
among neighboring AAs cause the strand to fold over on itself in
specific ways. The folded strand is a protein. Different AA sequences
will make different proteins.
Protein
•  Proteins interact with other substances
(including other proteins) in specific ways that
are determined by their electrochemical
properties.
•  There are only 20AAs out there—a finite
number (though in actuality the story is more
complex than this)
•  Different lengths and permutations of the AAs
that make up AA strands can lead to
countless varieties of proteins
Protein Functions
•  Structural proteins (collagen in skin, keratin in hair
and nails, proteins that make up muscle tissue, etc.)
•  Transport proteins (hemoglobin is a blood cell protein
that transports oxygen to body tissues)
•  Enzymes: proteins that catalyze (speed up) chemical
reactions in the body
•  Immune functions
•  Signaling functions: E.g., neurons in your brain
communicate with each other; these neurons are
proteins (and other substances)
Proteins
•  From where to organisms get the AAs
needed for body maintenance and
growth?
Food!
•  Foods are typically living
(or formerly living)
substances…
•  What substances are in
our food?
Lichtenstein 1962 Meat
Organismic Components
•  Organism = a living thing
•  Protein: the stuff living things are made of, including
structural proteins like collagen, enzymes, etc.)
•  Also water, carbohydrates, fats, vitamins/minerals,
DNA (nucleic acids), etc.
•  Proteins are long molecules that folded over on
themselves
•  The components of protein molecules are smaller
molecules called amino acids (AAs)
Proteins to AAs
•  Organism A eats foreign protein that makes up Organism B
•  Organism A breaks Organism B proteins into its constituent
AAs: digestion
•  Organism A s DNA restrings raw AAs up into Organism A
proteins
•  Organism A s DNA = blueprints for this protein synthesis
•  Organism B’s AAs = raw building blocks of proteins
Amino Acids to Proteins
…genes
Genes
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Proteins
Genes determine what proteins get built from those raw AA molecules
Genes are protein-coding units of DNA
You eat proteins of other living things, and break the protein into amino
acids; then, genes in your DNA re-string those amino acids into
proteins that YOU need to survive and reproduce
Bodies are made of proteins (fat and carbs and water are essentially
there to service these proteins)
Genes also code for enyzmes, which are proteins that regulate
everything, including development
Other parts of DNA do not code for proteins, and have either no
function (e.g. hitchhiker DNA), or function for self-regulation, and other
tasks—take advanced biology classes to learn about these very cool
things DNA does
What is DNA?
DNA
•  Deoxyribonucleic acid
•  A long molecule with a small number of constituent molecules
•  Shape is a double helix —think of a ladder that is twisted
DNA
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A sugar-phosphate
backbone, (I.e., the
sides of the ladder), and
rungs” made up of paired
nucleic acids
There are 4 nucleic acids:
adenine (A), thymine (T),
cytosine (C), and guanine
(G) [don’t worry about uracil
(U), for the purposes of this
class
Note these are not AAs
A only bonds to T
C only bonds to G
A-T and C-G bonds are weak
Sugar-phosphate bonds are
strong
Lots of zipping action
Genes to Proteins
•  Protein synthesis
•  An elegant process…that we will not go over in this
class (RNA, Uracil, ribosomes: do not worry about these for this
class)
•  Upshot: the sequence of nucleotides in DNA
determines the sequence of AAs in protein
manufacture (nucleic acid sequence maps to AA
sequence, but not one-to-one, and redundancy is
built into the system)
•  In other words, your DNA determines what proteins
get built out of the AAs that your body extracts from
the foreign proteins you eat
Genes
Proteins
Bodies
+
DNA
molecule
Amino acid
molecules
Cell parts, cells, and tissues
Amino acid strand
Organ
Protein
Body
Genes (DNA segments)
•  Genes are protein-coding regions of an organism s DNA
•  (1) They direct protein synthesis
•  (2) They ALSO replicate, or reproduce, over generations, as
they are passed from parents to offspring (offspring inherit
their parents genes)
–  (a) in single-celled organisms, one mother (or parental )
cell s genes double then divide and are passed on to two
daughter (or offspring ) cells (the parent cell no longer exists
—its body s proteins now make up the bodies of two offspring)
–  (b) in multicelled organisms, there are two kinds of cells: somatic
cells and germ cells:
•  (i) somatic cells (such as human skin cells), live only as a part of the parental
body; somatic cell genes build proteins for the parent s body; reproduction of
somatic cells involves gene replication, but the new cells remain a part of the
parental body
•  (ii) germ cells (such as sperm and eggs) are housed in the parental body; then,
at the time of reproduction, a germ cell leaves the parental body, anddevelops
a new multicelled body of its own
•  THE point: only germ cell genes can make it into the next generation for
multicelled organisms like humans
freshwater paramecium
(single-celled)
red-tailed hawk
(multicelluled)
Reproduction in
Single vs. Multi-celled Organisms
single-celled mother
multi-celled mother
Somatic line cells
All genes reproduce
by doubling
½ of reproduced
genes passed to
each of two
identical, singlecelled daughters
Germ line cell
*The somatic line cells ARE the
germ line cells
multi-celled daughter
At reproduction, germ line cell leaves
mother s body and multiplies, creating new
somatic cells for its daughter body, and, at
some point, a subsequent germ line of cells
that the daughter can transmit into the next
generation; germ line = eggs and sperm in
sexually-reproducing species
Germ line cell…
Genes vs. Alleles
•  Genes: protein-coding regions of an
organism s DNA
•  Alleles: different forms of a gene at
a particular spot ( locus ) on the
DNA; different allele sequences
make slightly different versions of a
protein, but ultimately different
alleles ore more-or-less functionally
similar
•  Here, the gene = eye pigment; with
a few exceptions, we all have eye
pigment, and the gene for this
pigment is at the same spot on out
DNA strand for every person
•  Allele = green eyes vs. blue eyes:
even though we all have eye
pigment protein, different people can
have different versions of the eye
pigment protein
white flowers=TGACCGATA
purple flowers=TGACCGACA
Allele Frequencies
•  Allele frequency = the proportions of different alleles
among all the individuals in a specific population
(in this room, allele frequencies underlying eye color might be
different from frequencies in a Scandinavian population,
which might have more blue and green eyes people, or a
population living near the equator, which might have more
brown eyed people)
•  Whiteboard exercise on allele frequencies of eye
color in this class, in order to illustrate what evolution
is…
Exercise:
Eye Color Allele Frequencies
•  100 people in class (assume, for now, that human eye color is
determined by a single gene with 3 possible alleles: brown, blue,
and green)
–  60 people have brown eyes
–  30 people have blue eyes
–  10 people have green eyes
•  The current generation of our classroom population, G1, has
the allele frequencies: 60% brown, 30% blue, and 10% green
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Everyone has the opportunity to reproduce. Many of us do. The
next generation s allele frequencies are…
Exercise:
Eye Color Allele Frequencies
•  The allele frequencies in the next generation, G2, are…
•  …again 60% brown, 30% blue, and 10% green
•  This means that allele frequencies have NOT changed over
generations: evolution has NOT occurred from generation 1 to
generation 2.
•  Now this 2nd generation has the opportunity to reproduce. Many
do. The allele frequencies in the next generation, G3, are…
Exercise:
Eye Color Allele Frequencies
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The next allele frequencies in G3 are…
now 90% brown, 5% blue, and 5% green
(they had been 60% brown, 30% blue, and 10% green in G2)
This means that allele frequencies HAVE changed over
generations: evolution HAS occurred from G2 to G3.
•  Evolution is defined as a change in allele frequencies in a
population over generations
Exercise:
Eye Color Allele Frequencies
•  G3 allele frequencies are 90% brown, 5% blue, and 5% green
•  Now this generation has the opportunity to reproduce. Many do.
The next allele frequencies in the next generation, G4, are…
•  90% brown, 5% blue, 4% green, and 1% purple
•  This means that allele frequencies HAVE changed over
generations: evolution HAS occurred between G3 and G4.
•  But where did this new purple allele come from?
Mutations!
•  Where do new, different alleles come from? Mutations.
•  Mutations are random mistakes in the molecular sequence of DNA,
which can lead to changes in proteins that get built
•  A change in the DNA sequence of a gene will cause a change in the
protein that gets built
–  ATGCAAAATCGG=green eye pigment protein
–  ATGCAACATCGG=purple eye pigment protein
•  Origins of mutations include radiation (x-rays, solar rays, other cosmic
rays, nuclear waste), various non-living substances (asbestos, cigarette
smoke), living substances (viruses), unknown causes, etc.
•  Only heritable mutations are relevant to the evolutionary process
because evolution is a process that occurs over generations
•  Not all mutations that occur in living things are heritable; there is an
important difference in the heritability of mutations in multi-celled vs.
single-celled organisms...
Heritability in
Multi-celled Organisms
•  Mutation must be in germ
line of cells to be passed to
offspring; only mutations in
the germ line heritable, and
thus subject to the process
of evolution
•  Mutations in the somatic line
can lead to new proteins
(usually bad) being built in
the maternal body
( cancer ), but these alleles
are NOT passed to the next
generation; they die with the
mother s body
Germ line cell
Heritability in
Single-celled Organisms
X-ray radiation
causes a
mutation in this
parental gene
(green)
x"
Somatic and germ line are the
same, so all mutations in parent
will be passed to offspring; that
is, all mutations are heritable
Mutations
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Mutations impact evolution in different
ways based on what types of cells they
are in; for multicalled organisms:
–  Somatic cell = maybe cancer—bad for
survival, but questionably bad; and may
or may not impact reproduction…or not
cancer
–  Germ line = Potentially very important
to reproduction (not survival) and the
physical process of natural selection
Evolution
•  Heritable alleles are passed from parent to
offspring over generations.
•  Evolution is change in allele frequencies in
a population over generations.
•  Natural Selection is one type of evolution
(there are 4…)
Definitions and Types of
Evolution
•  There are 4 causes of changes in the allele
frequencies in a population over time:
–  (1) Migration of individuals in or out of a population can cause the
allele frequencies to change (e.g., a bunch of red eyed people join
our population in the next generation)
–  (2) Mutations can cause allele frequencies to change (e.g., one
person s child happens to be born with a mutated allele that
produces purple eyes)
–  (3) Genetic drift occurs when a random event NOT related to
one s alleles alters the allele frequencies in a population (e.g., the
5 blue eyed people in our population happen to fall off a cliff,
erasing all blue genes from the subsequent generation—and
having blue eyes had NOTHING to do with falling)
–  (4) Natural selection…
Natural Selection
•  Natural selection is change in allele
frequencies in a population over
generations due to the causal effects
alleles have on reproduction
Natural Selection
•  If reproducing entities exist, if variations are heritable, and if
variations have reproductive consequences, then over time,
the entire population will come to possess the reproductively
superior variation
–  *note that for multicelled organisms, these variations are in the germ
line of cells
•  In terms of genetics: Over generations, alleles that build
proteins that promote their own reproduction relative to the
rest of the alleles in the population will reproduce more than
the population’s alleles that build proteins that hinder their
own reproduction.
•  Simple, and NOT circular, as time only goes in one direction.
Within- and Between-Species
Competition
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A common misconception when
thinking about natural selection
Competition or a struggle for
existence among members of
different species
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(misconceptions of Survival of the
Fittest notions…)
E.g., thinking about rabbits vs.
foxes (thought experiment—then
why are there still any rabbits
around?...)
Or thinking about a species vs.
the many environmental
circumstances that it encounters,
including other species
Not just getting food from the
environment...
Getting more food than other members of
your species from it
Not just avoiding predators…
Avoiding predators better than other
members of your species
Not just avoiding parasites…
Parasitic micro-organisms: roundworm, protozoan, bacterium, fungus, yeast
Avoiding parasites better than
other members of your species do
(mange; a funny website:
http://www.giantmicrobes.com/)
Not just getting good living spaces...
Wedge tail eagle nest
Getting better living spaces than other members of your
species ( strumming, Riechert & Hammerstein)
Funnel spider
Stay Away from Funnel Spiders
Don t think of it as the environment (which
includes other species) vs. the mouse
Think of it as mouse vs. mouse in a particular
environment (which includes other species and
also NONliving things!)
Mouse vs. mouse
•  In any population,
not all individuals
survive to reproduce.
Found place to live.
Out-competed other mice for food.
Found a mate.
Successfully avoided predators.
Reproduced successfully.
His kids inherited his genes and the
traits those genes build.
No place to live.
No food.
Couldn t find a mate.
Predator ate him.
Did not reproduce.
His nonexistent kids did
not inherit his genes and
the traits those genes
build.
Important for mammals, and highlights the
importance of within-species competition to exist
and to reproduce: getting more or better mates
than other same-sexed members of your species
Male red deer
Within-species Competition:
The Bear and the Campers
Warning
For the good of the
species
-Thought experiment: who would reproduce more, an organism that
incurred a cost on its own reproduction to benefit others in its species,
or one that hurt others to benefit its own reproduction?
Still within-species competition, even here, where different
species are still in different niches even though they are all eating
the same fallen gazelle
(1st cheetah, 2nd lions, 3rd hyenas, 4th vultures, next bugs…)
Issues with and
Misunderstandings about Evolution
•  Many exist, and historically they have even had abominable impacts
on human lives
•  Many misconceptions involve lacking relevant background
knowledge about biology
•  Many involve trying to tie evolutionary principles to moralistic
frameworks
•  Many involve challenges that materialist, evolutionary accounts
might pose to deeply-held beliefs in nonmaterial or supernatural
accounts of life
•  In academia, many involve challenges to deeply-held assumptions
about nature vs. nurture
•  These are beyond the scope of this class, but…
•  At least one misunderstanding can be traced to the problematic
phrase survival of the fittest …
Survival of the Fittest
•  A phrase introduced by H. Spencer in the 1800s to justify the
oppression of so-called inferior populations; based on a
misinterpretation of Darwin s theory of natural selection; caused
a LOT of horrible acts in human history
•  Problematic terms and meanings:
–  Survival? Nope, it is actually reproduction that is relevant--salmon
die to spawn; birth kills 1/100 women in regions without access to
medical care; men risk their lives in fights over women; male
praying mantises are eaten alive by the female during copulation
–  What does fittest mean? The strongest? The fastest? What about
the rodent-like mongrels that survived the meteor that killed off the
dinosaurs 65 million years ago?...the mongreals that are our
ancestors!
–  Fittest? Fittest what? Fittest species? Fittest group? Fittest
individual? Fittest genes? Fittest ecosystem?
Survival of the Fittest
•  Typically, laypeople think the phrase survival of the fittest
explains why certain species dominate other species, and
that it s misconstrued meaning justifies the painful suffering
we see endured by some organisms to the benefit of other
organisms: e.g., when we see a gazelle get hunted and
eaten by a cheetah (cheetahs being the more "fit species),
we say that is nature s way—survival of the fittest ;
additionally we see and justify the suffering of within-species
conflict that guy won the fight, thus survival of the fittest
•  This is NOT a moral thing. It is just a way to try to
understand why the organisms we can observe have the
features they do. Period.
end