1. 1. The scientific process involves…
A. the acceptance of all hypotheses.
B. rejection of hypotheses that are inconsistent with experimental results.
C. the acceptance of only data consistent with the hypothesis.
D. the acceptance of hypothesis as a fact even after subsequent non-confirmation with experimental results.
E. the formulation of theories without experimentation or obtaining proof.

2. 2. Gingko trees lose leaves every Fall season
2. Gingko trees lose leaves every Fall season. These trees may lose their leaves in response to decreasing day length.  The italicized sentence is an example of…
A.  deductive reasoning
B.  an experiment
C.  a hypothesis
D.  inductive reasoning
E.  a theory

3. 3. Which of the following is a good example of hypothesis-driven research?
  A. You are interested in studying the effect of chocolate consumption on test grades. You hand out a chocolate bar to half of the people in the class and instruct them to eat it immediately prior to taking the test. After the test you analyze the grade distribution to see how grades were affected by chocolate consumption.
B. You are interested in studying the effect of chocolate consumption on test grades. You hand out a chocolate bar to everyone in the class and instruct them to eat it immediately prior to taking the test. After the test you analyze the grade distribution to see how these grades differed from the last exam when no one ate any chocolate.
C. You propose that the consumption of chocolate immediately prior to taking the biology midterm will result in a high grade. You hand out a chocolate bar to half of the people in the class and instruct them to eat it immediately prior to taking the test. After the test you analyze the grade distribution to determine if students who ate chocolate got higher grades than students who did not eat chocolate.
D. You decide that the consumption of chocolate immediately prior to taking the biology midterm will impact grades. You hand out a chocolate bar to everyone in the class and instruct them to eat it immediately prior to taking the test. After the test you analyze the grade distribution to see how these grades differed from the last exam when no one ate any chocolate.

4. The three major domains of Life on Earth are:
The Plants, the Animals, the Bacteria
The Protists, the Bacteria, the eukaryotes
The Bacteria, the Archaea, the Eukaryotes
The Archaea, the Plants, the Animals

5. 6. The same basic array of bones is modified to give rise to the wing of a bat and the fin of a porpoise. Such features are called…
A. analogous. B. uniform. C. homologous. D. inherited. E. evolutionary modifications.
7. Organismal features that have similar structure and function but different evolutionary origins are called… 
A. homologous. B. analogous. C. inherited. D. uniform. E. evolutionary modifications.

6. Phylogenetic analysis has revealed that in vertebrates and insects, eyes are analogous, rather than homologous, structures. Interestingly, however, more recent molecular genetic analysis determined that the homeodomain protein Pax6 is a key regulator of eye development in both vertebrates and insects.
4. Analogous structures  A. have the same evolutionary origin, structure and function. B. have similar functions and evolutionary origins, but differ in structure. C. have the same evolutionary origin, but now differ in structure and function. D. have similar functions, but different evolutionary origins.
   
5. The function of Pax6 in eye development can be viewed as an example of  A. an emergent property. B. evolutionary conservation. C. comparative anatomy. D. natural selection.

7. Birds
Bats
Evolution of four limbs
Evolution of tetrapod
flight

8. An Information Flow in Biology Primer
replication (mutation!)
genes
DNA
Nucleic acids ~
“software”
(nucleotides)
transcription
messages
RNA
(nucleotides)
translation
Protein
(amino acids)
~ “hardware”

9. Chapter VI
…Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.…
Charles Darwin, The Origin of Species

10. Chapter VI
…Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. …
Chapter VI
…Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree.
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. …
Chapter VI
…Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree.
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possesser, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. …
Chapter VI
…Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree.
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. …
Chapter VI
…Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree.
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. …
Chapter VI
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possesser, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. …
…Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree.

11. Chapter VI
Chapter VI
Chapter VI
Chapter VI
Chapter VI
Chapter VI

12. Chapter IV
Chapter IV
Chapter IV
Chapter IV
Chapter IV
Chapter IV

13. Protein A Protein B Species 5 GNAGYGAEALERM Species 6 GNAGYGAEALERM
Species 6 GNAGYGAEALERM
Species 2 NHAAFGAEALERM
Species 3 NHSAYGAEALERM
Species 1 AHAGYGAEALERM
Species 4 GHAGYGGEALDRT
Species 5 LCNSIGSLFQTFSI
Species 6 LCNSTGSLFQTFAI
Species 2 LCNSTGSLFQTFAI
Species 3 LCNSTGSLFQTFAI
Species 1 LCNSIGSLFQTFSI
Species 4 LCNSIGSLFQTFSI

14. A B C

15. Discuss! Discuss your answer in your group; what strategy did you use?
Do you want to change your answer? Two minutes! 4 1

16. Species Key
species 1 = Human
2 = Sperm Whale
3 = Dolphin
4 = Dog
5 = Fruit Bat
6 = Horseshoe Bat
• write the species names out on the tips of your best-supported tree

17. Why might data from these two genes support different hypotheses: write list on table
What kind of evidence/information would help you distinguish between your different ideas?
Feel free to ask DM for help

18. Two genes (proteins) determine different phylogenetic relationships
Hemoglobin
Transports oxygen in Red Blood cells
Highly conserved
Prestin
Inner ear motor protein
Role in high frequency sound detection
Certain variants important in acquisition of echolocation
news.rice.com

19. What evolutionary process best explains the dichotomy?
convergent evolution in prestin;echolocation evolved twice – prestin function is analogous in bats and whales
B. convergent evolution in globin; echolocation evolved once – prestin function is homlogous among whales and echolocating bats
echolocation
echolocation
echolocation

20. Fig. 1.14