Option D: Evolution
Rushka and Alex
D1:
Origin of Life on Earth
D.1.1: Four processes needed for the spontaneous origin of life on Earth:
  • the non-living synthesis of simple organic molecules-
In the early Earth, there are only two sources for organic molecules: terrestrial and extraterrestrial origins. Organic synthesis is simply chemical reactions used in order to determine the organic compounds that make up the molecule.Terrestrial origins refers to when the organic synthesis is activated by impact shocks and ultraviolet rays. Extraterrestrial origins refers to when there is a gravitational attraction of organic molecules or primitive life-forms from space.
  • the assembly of these molecules into polymers-
Polymers are macromolecules made up resembling a chain and held together by covalent bonds. Polymers help build up amino acids which eventually become proteins.
  • the origin of self replicating molecules that made inheritance possible-
By replicating itself, more and more proteins build up eventually becoming an organism.
  • the packaging of these molecules into membranes with an internal chemistry different from their surroundings-
After organisms are formed, bigger living things develop and start adapting itself in order to survive in it's environment. Example: Cacti can retain water despite it's dry environments because they have adapted in order to survive.

D.1.2: Miller and Urey experiment was mainly about finding out how life on Earth really started but more specifically, they tested Alexander Oparin's and J. B. S. Haldane's hypothesis that the conditions on early Earth were more favorable to chemical reactions that synthesized organic compounds from inorganic ones. When their experiments were finished, new scientists testing their equipment realized that there was actually 22 amino acids formed altogether rather than the mere 5 that Miller and Urey thought they found.

D.1.3: Comets may have delivered organic compounds to Earth. Comets contain a variety of organic compounds both simple and complex. A bombardment about 4000 million years ago probably brought organic compounds and water to Earth. Cometary organics are formed in interstellar dust (ISD) environments. Another things necessary for the start of life on Earth formed in ISD environments are a wide variety of amino acids and pyrimidine bases(uracil, cytosine, and thymine)!

D.1.4: Locations where conditions would be in favor of the synthesis of organic compounds: Organic compounds in the primitive oceans are formed by ultra violet solar radiation. At volcanoes, organic compounds are formed by solar energy.

D.1.5: Two properties of RNA that allow it to have a role in the origin of life:
RNA or ribonucleic acid can do two things: store information, like DNA, and act as an enzyme to catalyze reactions. Storing information definitely helped with the origin of life because it helped with inheritance of genes that influenced adaption and therefore evolution. Acting like an enzyme also helped with the origin of life because it is necessary to make amino acids and hence proteins. It is also said that RNA paved the way for DNA to become possible.

D.1.6: Living cells may have been preceded by protobionts with a internal chemical environment that is different from it's surroundings.

D.1.7: Prokaryote's contributions to the creation of the oxygen rich atmosphere: Prokaryotes use photosynthesis with other organic materials to make energy. Photosynthesis produces oxygen in the air.

D.1.8: Endosymbiotic theory for the origin of eukaryotes: The endosymbiotic theory is that the mitochondria of the eukaryotes developed from aerobic bacteria living in the host cell and that the chloroplasts of eukaryotes evolve from endosymbiotic cyanobacteria.

D2:
Species and Speciation
D.2.1:
Allele frequency- the frequency of occurrence or proportions of different alleles of a particular gene in a certain population.

Gene pool-total genetic information in the gametes of all individuals in a certain population.

D.2.2: Evolution involves a change in allele frequency in a population's gene pool over a number of generations because of the combinations of different genes.

D.2.3: Species- the important division of a genus or subgenus, species is the most basic category in biological classification, can mate among themselves but not out of their specific species category.

D.2.4: Three examples of barriers between gene pools.
  • geographical isolation- when a species is separated by geography, barriers are formed in the gene pools because both parts of the species begin to adapt to their new environment, causing a split, forming 2 separate species.
  • hybrid infertility- when a hybrid is produced, fertility problems occur because two separate types of gene pools were trying to mix. This affects the gene pool because those hybrids can't pass their traits to offspring.
  • temporal isolation- when there is a temporary isolation problem within a species. When the isolation is fixed, depending on the time the specie had separated, they can probably never mate again because they had already begun to adapt. Again 2 species are formed.
  • behavioral isolation- an isolation process where two different species don't mate because of different courting habits.

D.2.5: Polypliody is when the total number of chromosomes in a cell is doubled. This can happen when two species try to mate and also by mutations. This can result with the animal or plant not being able to reproduce, or it can result in a plant that is both male and female meaning it can provide for itself. Most of the angiosperm species have originated this way.

D.2.6: Compare Allopatric and sympatric speciation
  • speciation- the formation of a new species by splitting an existing species.
  • sympatric- in the same geographical area.
  • Allopatric- in different geographical areas.
Sympatric speciation is when there is a formation of a new species from splitting one in half in one geographical area. Allopatric speciation is splitting a species in two from different geographical areas. I believe that allopatric speciation is better than sympatric speciation because when I species is split geographically before this, they are already going to have new mutations and adaption. if it is in the same geographical area, and they are forced to split, a whole new species will be formed.

D.2.7: Adaptive radiation process started with natural selection but is fast evolutionary radiation causing phenotypes to change based on the environment. Example: finches at the Galapagos Islands.

D.2.8: Convergent evolution- when two different species with no common ancestors share a similar trait.
Divergent evolution- when a group in a population develops a new species.

D.2.9: Gradualism is the slow change from one form to another not noticeable over a short period of time. Example: how humans evolved to how we are now. Punctuated equilibrium is about short periods with rapid evolution. Volcanic eruptions are punctuated and meteor impacts affecting Earth are very gradual.

D.2.10: One example of transient polymorphism: industrial melanism. Melanism is when there are dark pigments in skin, hair, feathers, eyes, etc. Transient simply means over time and polymorphism means a stop in genetic variation where two or more forms, stages, or types exists within the same species.

D.2.11: Sickle-cell anemia is an example of balanced polymorphism where heterozygotes have an advantage in malaria regions because they are fitter then both homogzygotes. This is because the heterozygotes hold the sickle-cell gene and hence the malaria can't effect them(because of the shape of their blood cells, it can't hold the malaria.)

D3:
Human Evolution
D.3.1 To determine the ages of rocks one method is through Radiocarbon dating. Organic material is trapped within a part of a rock/part of a rock and/ or fossil. This material contains the isotope of carbon-14. When plants fix atmospheric carbon dioxide, the carbon dioxide levels within them match the outside isotopic levels of carbon-14 so that when the plant dies, is consumed, fossilized, etc. the amount of C-14 begins to decline in an exponential rate. Comparing this exponential decay with the expected amounts of C-14 isotope levels during that time can help scientists figure out how old rocks or fossils can be. Carbon-14 is used because the half life of the isotope is only about 5,730 years which is relatively small compared to other, however Carbon-14 is not entirely accurate due to the fact that there are many outlying factors that could contribute to a spike in carbon levels during the time that the organic materials dyed , such as: volcanic activity, and other big events could give off high carbon levels which could lead to inaccurate events and now with our global climate changing so drastically and pollution, the carbon in our atmosphere has increased so much that the accuracy of carbon dating has lessened by a few percent just in the last few years. Furthermore the carbon-14 isotope is only able to ‘accurately’ determine rocks of a certain age. Assuming that the earth is approximately 3.2 billion years old, carbon dating wouldn’t be suitable for all ages of rocks. So the isotope potassium-40 is used because it’s half life is about 1.3 billion year, big enough so that the oldest igneous and metamorphic rocks can be dated.

D.3.2 Half Life: the amount of time it takes for half the nuclei of an isotope to undergo radioactive decay.

D.3.4 Humans are Primates because they have: generalized limb structure with five digit on extremities, flattened nails rather than claws, the face is short: no long snout (comparatively speaking), a lesser sense of smell, emphasis on vision, a bony separation in between the primate orbit and temporalis muscle, they have an elaborate placental tissue connecting the infant and mother, the size of a brain is directly relative to the size of your body, three types of teeth, two separate bones in arm and leg.

D.3.5 Hominid Species
Ardipithecus ramidus:Has been dated to 5.8 million years old. The distribution of the species is unknown, because while ‘ramidus’infers that the creature was a forest dweller scientists contend that in order for a species to become bipedal it would have been more likely that the creature would exist in a more savannah like environment.

Australopithecus
A.Afarensis: existed between 3.9 and 3.0 million years ago and was found within Eastern Africa
A.Africanus: lived between 2-3 million years ago. Remnants of the species were found in only four sites in South Africa.

Homo
H. habilis: existed 1.5-1.4 million years ago found in Tanzania East Africa.
H. erectus: 300,000-1.8 million years old and was found to have been in Afric originally but then moved to as far as China and Java.
H. neanderthalensis: existed between 30,000-230,000 years ago. Found in parts of Europe, western Asia and Central Asia.
H. sapiens: first appeared around 195,000 years ago. H. sapiens are found dispersed all over the globe

D.3.6 See picture diagram to see how some species of hominid may have coexisted.
timeline.jpg
D.3.7. Reasons for Fossil Record Incompleteness:
  • The enviroment that the organisms died in may not have been conducive to fossil creation.
  • movements of the earth's fault lines make it so things like deep sea creatures are seldom recovered or found.
  • A lot of the fossils, we just can't get too.
  • some organisms infrastructure is not hard enough to face the erosion or constant environmental hardships.
  • There are very specific ways in which a fossil must be produced and the simple fact is that only a small portion of evolutionary organisms are represented through fossils.
Because fossils have so drastically changed the way we view the world it begs the question is we have or if we should put so much emphasis on something will such a small pool of evidence
D.3.8

As you can see from the table below: the younger the species the more directly higher the intelligence is associated with body mass
fossil_hominin_brain_percent_lg.png
D.3.8 continued.....
  • You can observe that earlier hominids had smaller brains/ brains closer to that of ape's brains and you can conclude from their teeth that their diet consisted of mainly vegetation
  • 2.5. million years the savanna grasslands replaced the forests in Africa so therefore the diets of those hominids changed and that changed coincided with a great evolution
  • in early hominids that had a certain diet the developments of infants was a much slower process AS OPPOSED to nowadays with our current diet our infants develop a lot faster
  • explanation: the proteins, fats and lipids found within meat that was introduced to Hominid diets promoted brain growth

D.3.9
The basic difference between genetic and cultural evolution is the difference between nature and nurture. Genetic evolution occurs through a need for extreme adaptation due to environment. Change is random through mutations and is hereditary/ passed down through DNA. Genetic evolution also occurs gradually throughout generations. Cultural evolution is is independent from DNA and is is dependent on intelligence and curiosity. Can occur at anytime and does so much more rapidly that a genetic evolution.

D.3.10 While genetic evolution moves the species and organisms further and betters the species in a more physical manner, genetic evolution would be obsolete if it was not used or utilized in some way due to cultural evolutions. Genetic evolution gives us a greater brain capacity and intelligence but if we don't exercise this gift through exploration, inquisitiveness and exploration there would be no point and the evolution would not continue/ those traits which seem so important to us now would never get passed on.

D4:
The Hardy-Weinburg Principle
"D.4.1 Explain how the Hardy-Weinberg principle is derived.
  • frequency of dominant allele, A = p
  • frequency of recessive allele, a = q
  • total of both alleles, p + q = 1.0 (1.0 = 100% of the population; therefore, p and q must be values between 0 and 1.0; e.g. 0.5 means 50% of the population)
  • calculate the frequency of each genotype through Punnett square
p (A)q (a)

pp2 pqfrequency of AA = p2
(A)(AA)(Aa)frequency of Aa = 2 pq
frequency of aa = q2
qpqq2
(a)(Aa)(aa)
  • determine the frequencies of alleles in the first filial generation
p + q = 1.0

(p + q)2 = 1.0

p2 + 2pq + q2 = 1.0
  • the Hardy-Weinberg principle allows us to see that, allelic frequencies will remain constant from one generation to the next, under certain conditions
AA : Aa : aa = p2 : 2pq : q2
D.4.2. Calculate allele, genotype and phenotype frequencies for two alleles of a gene, using the Hardy-Weinberg equation.
  • given that red eyes are dominant and white eyes recessive in Drosophila, and that 64% of individuals are normal winged, 36% vestigial-winged, determine the genotypic and phenotypic frequencies of the two alleles, assuming that all Hardy-Weinberg conditions are met
vg+ = allele for normal wings; p = frequency of vg+
vg= allele for vestigial wings; q = frequency of vg; q2 = frequency of vg/vg
  • given that q2 = .36
q = 0.6 ( q = √0.36)
p = 0.4 (p = 1 - q; 0.4 = 1 - 0.6)
p2 = .16 (p2 = 0.4 x 0.4) thus, 16% of population = vg+vg+ (homozygous)
with normal wings
2pq = 0.48 (2pq = 2 x 0.4 x 0.6) thus, 48% of population = vg+vg
(heterozygous) with normal wings
D.4.3 State the assumptions made when the Hardy-Weinberg equation is used.
  • If the frequency of alleles A and a in a parental generation are p and q, then p + q = 1 and in future generations AA : Aa : aa = p2 : 2pq : q2
  • Hardy-Weinberg conditions:
  • population is large (reducing effects of genetic drift, i.e. chance)
  • mating must be random
  • no mutation
  • no selection
  • no emigration or immigration (no gene flow)"


D5:
Phlyogeny and systematics
"D.5.1 Outline the value of classifying organisms.
Taxonomy = the science of classification: arranging organisms into groups, which provides several advantages:
  • species identification: members of a species share nearly all the same characteristics
  • predictive value: groups of related taxa share many common characteristics
  • evolutionary links: shared derived characteristics are inherited from common ancestors
  • effective communication: all scientists use the same terminology for taxonomy
Taxonomy uses both morphological and biochemical methods to distinguish homologous structures from analogous structures
  • avoids the problem of convergence, in which unrelated organisms have similar morphologies, called analogous structures
  • emphasizes homologous structures which are those derived from a common ancestor
D.5.2 Explain the biochemical evidence provided by the universality of DNA and protein structures for the common ancestry of living organisms.
DNA structure is universal, i.e., the same in all organisms, composed of polymers of the same four nucleotides: adenine, guanine, cytosine, and thymine
mRNA, rRNA, and tRNA are universally used in protein synthesis, RNA is composed of the same four nucleotide: adenine, guanine, cytosine, and uracil
Ribosome structure is universal, composed of large and small subunits, each composed of proteins and rRNA, and providing a site for mRNA attachment and two sites for tRNA attachment
Protein structure is universal, composed of polymers made of the same 20 amino acids
Genetic code is universal: The genetic code whereby DNA is transcribed into RNA and then translated into proteins is universal, so that all organisms use the same codons for determining amino acid sequence
ATP is the universal energy molecule: commonly used to provide energy for chemical reactions in all organisms
Amino acids are L-form isomers in all organisms
  • (Optical isomers are molecules that are mirror images of one another, known as D- and L- forms)
Carbohydrates in DNA and RNA are D-form isomers in all organisms
Glycolysis is universal, the common biochemical pathway by which glucose is hydrolyzed to produce ATP
Membranes are universal, fluid mosaics of proteins within a phospholipid bilayer
Summary: because all of the basic biochemistry of genetic information, protein synthesis, cellular organization and energy transfer is near identical in all organisms, they likely inherited it from a common ancestry
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D.5.3. Explain how variations in specific molecules can indicate phylogeny.
Differences between molecules can be used as part of the evidence to deduce phylogenetic relationships
  • phylogeny = the evolutionary history of a taxonomic group, often shown in a phylogenetic tree
  • mutations in DNA occur with predictable rates
  • differences can be used as a molecular clock to develop phylogeny
    • DNA nucleotide sequences
    • protein amino acid sequences
Globins: hemoglobin and myoglobin
  • globin genes are present in all animals and some plants
  • the greater the similarity in the globin genes of two species, the less time has passed during which mutations could accumulate, and thus, the degree of similarity can be used as a measure of how closely related the two species are
  • the greater the similarity in a protein produced by two species, the more recently they shared a common ancestor
  • the greater the difference in a protein produced by two species, the more distantly they shared a common ancestor
D.5.4. Discuss how biochemical variations can be used as an evolutionary clock.
Differences in nucleotide base sequences in DNA, and therefore amino acid sequences in proteins, accumulate gradually over long periods of time
  • differences accumulate at roughly constant and predictable rate
    • therefore, the number of differences can be used as a clock
    • to measure the time since two divergent groups shared a common ancestor
  • however, variations are partly due to mutations
    • which are unpredictable chance events
    • so there must be caution in interpreting data
Hemoglobin varies between vertebrates: Hemoglobin, a blood protein found in all vertebrates, shows amino acid differences compared to humans in of a variety of vertebrates:
  • horse: 18
  • mouse: 16
  • reptile: 35
  • frog: 62
  • shark: 79
Calibrate variation to time: Hemoglobin amino acid differences correlate to geological time based on fossil record:
  • mammals: originated 70 million years ago
  • reptile: originated 270 million years ago
  • frog: originated 350 million years ago
  • shark: originated 450 million years ago

Establish a variety of molecular clocks:
  • Hemoglobin changes at a regular rate over hundreds of millions of years, acting as a molecular clock.
  • A variety of proteins have been studied, each producing its own molecular clock.
  • Histones (organize DNA) hardly change at all.
  • Cytochrome c (a mitochondrial protein) changes slowly.
  • Hemoglobin (blood protein) changes moderately.
  • Fibrinopeptides (clotting proteins) change rapidly.
D.5.5. Define clade and cladistics.
Clade: a group of organisms that evolved from a common ancestor
Cladistics: a method of classification of living organisms based on the construction and analysis of cladograms
Nodes: branch points indicating the evolution of shared derived characteristics
D.5.6. Distinguish, with examples, between analogous and homologous characterisitcs
Analogous characteristics: structures with a common function, but a different evolutionary origin
  • example: dolphin fins and shark fins
Homologous characteristics: structures that have a common evolutionary origin, even if they have different functions
  • example: dolphin forelimbs and human arms
D.5.7. Outline the methods used to construct cladograms and the conclusions that can be drawn from them.
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D.6.9. Analyse cladograms in terms of phylogenetic relationships.
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D.5.10. Discuss the relationship between cladograms and the classification of living organisms.
The classification of many groups has been re-examined using cladograms.
  • in many cases, cladograms have confirmed existing classifications, as expected, since both are based on phylogeny
  • in some cases, cladograms can be difficult to reconcile with traditional classifications
    • nodes can be placed at any point
    • making the fit of taxa to the cladogram arbitrary
  • insome cases, cladograms radically alter existing classifications
    • for example, birds are grouped within a clade including dinosaurs
The strength of cladistics is that the comparisons are objective, relying on morphological and molecular homologies
The weakness of cladistics is that molecular differences are analysed on the basis of probabilities
  • improbably events occasionally occur, making the analyses wrong"