1. Evidence for evolution
In the early 1800’s prevailing belief was that:
organisms were specially created and unchanged since their creation
Species created independently of each other
Earth not old. Ussher’s estimate: for Earth’s creation 4004 BC

2. Lamarck Fact of evolution proposed in late 1700’s early 1800’s.
Jean Baptiste Lamarck 1809, 1815 proposed that all species were derived by gradual evolution from other species.
Lamarck’s idea was that evolution was driven by an innate tendency of organisms to become more complex over time.

3. Inheritance of Acquired Characteristics
Lamarck’s proposed mechanism of evolution was called the Inheritance of Acquired Characteristics (IAC)
IAC suggested that modifications to organisms during their life could be passed on to their offspring (e.g., a giraffe stretching its neck during its life passes slightly longer neck to offspring).

4. Inheritance of Acquired Characteristics
Obviously, Lamarck’s ideas about the mechanism of evolution largely contradict current biological knowledge.
The information required to build a body is stored in DNA and that information (influenced by the environment) determines the phenotype. Changes to the phenotype during life however do not affect the DNA sequence. Information flow is thus only in one direction from DNA  phenotype, not in the reverse direction.

5. Epigenetics
However, recent research in the emerging field of epigenetics shows that Lamarckian effects may occur through changes in the control of gene expression caused by environmental effects e.g. food shortage during development.

6. Epigenetics
Epigenetics is the study of heritable changes in gene expression caused by mechanisms other than changes in the DNA sequence.
The DNA nucleotide sequence is not changed but whether and how much genes are expressed can be altered and some of these changes may be passed from one generation to another.

7. Epigenetics
One way in which epigenetic effects have been shown to occur is through environmentally induced methylation in which a methyl group (CH3) is added to cytosine nucleotides converting them to 5-methyl-cytosine.
More heavily methylated regions are translated and transcribed less frequently than non-methylated regions.

8. Epigenetics
One well documented example of epigenetic effects resulted from the Dutch winter famine of 1944/45 at the end of WWII.
The children of women pregnant during the famine were born smaller than normal (which was to be expected).
However, the children of those children were also born smaller than average. This suggests the famine induced epigenetic changes in mothers pregnant during the famine that were passed to their offspring.

9. Charles Darwin
published
“On the origin
of species”
in 1859.

10. Charles Darwin (1809-1882) Son of a wealthy doctor.
Dropped out of medical school.
Studied theology, but was much more interested in natural history (e.g. he had a large insect collection).
After college signed on as captain’s companion on The Beagle.

11. Voyage of the Beagle Darwin companion for Captain Fitzroy on
The Beagle’s mission was to map the coast of South America, but the ship traveled around the World.
Sites visited included Galapagos Islands a group of volcanic islands (hence of recent origin) off the coast of Ecuador.

13. Galapagos Giant Tortoise
Unique animals on Galapagos include
giant tortoises, marine iguanas, and
Darwin’s finches.
Galapagos Giant Tortoise

15. Sharp-
beaked
Ground
Finch

16. Influence of geological thinking on Darwin
By the time of “The Beagle” voyage the idea that Earth was young was being challenged.
Opposition based on principle of Uniformitarianism.
This is the idea that geological processes happening today are the same as have operated in the past.

17. Influence of geological thinking on Darwin
Uniformitarianism contrasted with Catastrophism which proposed that current geological formations had resulted from catastrophic events (such as the biblical flood) which occurred on scale unknown today.
Uniformitarianism first proposed by James Hutton and championed by Charles Lyell.

18. Influence of geological thinking on Darwin
During the voyage Darwin read Lyell’s new book “Principles of Geology.”
Lyell emphasized two points:
1. Gradualism: Geological features can be explained by the slow gradual action of processes we observe every day e.g. erosion by wind and water, deposition of sediments in rivers.
2. The Earth is very old: there has been lots of time for change to occur.

19. Influence of geological thinking on Darwin
Hutton and Lyell inferred Earth must be very old based on measurements of rate of ongoing rock forming processes (e.g. deposition of mud and sand).
These developments in geology focused Darwin on the potential importance of gradual change in shaping structures.

20. What Darwin observed
On the voyage Darwin noted many things that were puzzling from the point of view of a creationist explanation for the diversity of life.

21. What Darwin observed
1. South American fossils resembled living South American animals.
2. Parts of the world with similar habitats and climates (e.g. Australia and South America) are populated by very different animals.
3. Plants and animals on each continent are different from those on other continents.
4. Many species on remote oceanic islands are found only there (endemic).
5. Endemic species on islands closely resemble species found on adjacent mainland.

22. What Darwin observed
These observations taken together don’t make sense if organisms were specially created.
Why should similar habitats in different parts of the world have different faunas?
Why should remote islands have unique faunas that differ from but resemble those on adjacent land masses?
Together these observations suggested to Darwin that species change over time i.e., that evolution occurs.

23. Darwin and Wallace
After returning from the voyage Darwin spent more than 20 years developing his ideas and gathering the evidence to support them.
In 1858 Charles Darwin and Alfred Russel Wallace jointly proposed natural selection as the primary mechanism by which evolution takes place.
In 1859 Darwin published his book On the Origin of Species, which summarized his ideas about evolution and presented the evidence to support them.
Darwin was (rightly) concerned about the likely public backlash against is ideas. He delayed publication until forced to until 1858 when he received a letter from Alfred Russel Wallace a naturalist working in Indonesia, in which Wallace described the idea of natural selection, which he had developed independently of Darwin. Darwin could no longer delay and in 1858 Darwin and Wallace coauthored a paper read at the Royal Society that described the idea of natural selection as the mechanism of evolution.

24. The “modern synthesis”
Idea of evolution was accepted rapidly by scientists.
Lack of understanding of heredity and population genetics, however, prevented natural selection being accepted as the principal mechanism of evolution until 1930’s.
The “Modern Synthesis” in the 1930’s of combined the ideas of population genetics and natural selection to explain gradual evolution, speciation, and macroevolution.
Gregor Mendel figured out the problem of inheritance during Darwin’s lifetime, but his work was not discovered by scientists in general until the early 1900’s well after both Mendel’s and Darwin’s deaths.

25. Evidence for Evolution
Evidence of change in organisms over time
An example in a living species:
evolution of beak length in soapberry bugs.
Soapberry bugs use long beak to penetrate seeds in fruits and eat them.
Native host plant is balloon vine which has thick fruits.

26. Evolution of Soapberry Bugs
In 1926 flat-podded Golden rain tree introduced to Florida. Has thin fruits.
Today soapberry bugs feeding on Golden rain trees have much shorter beaks than those living on balloon vines.

27. Comparison of beak
lengths in areas
with and without
golden rain trees

28. Data from museum
specimens documents
change in beak length
over time.

29. Antibiotic resistance in bacteria
In 1947 only four years after the mass production of penicillin began resistant strains of Staphylococcus aureus began to be reported.
Antibiotic resistance is now widespread and in the US half of all S. aureus infections are resistant to multiple antibiotics including penicillin, tetracycline, erythromicin and methicillin.

30. Antibiotic resistance
Bacteria have evolved resistance quickly in part because of their rapid reproduction, but also because antibiotics were misused (e.g. by being overprescribed or prescribed for non-bacterial infections and by people not completing their course of antibiotics)

31. The evidence for evolution
Fossil evidence
Vestigial structures
Homologous structures
Atavistic structures
Other evidence
Jerry-rigged structures
Adaptive radiation
Artificial selection

32. Fossil evidence
Fossils are mineralized copies of the remains of organisms preserved in sedimentary rocks.
In the process of fossilization a dead organism is covered by sediment and the organic matter is replaced by minerals leaving behind an impression of the organism.

33. Fossil evidence of evolution
Millions of fossils have been collected and it is clear from fossil evidence that many species (in fact almost all that have ever existed) have become extinct.
Equally clearly the faunas of different geological eras are very different and have changed over time.

34. Fossil evidence of evolution
Law of Succession: Fossil and living organisms in same area are related to each other and differ from organisms in other areas.
South America contains both fossil and living armadillos

35. Extinct glyptodont (2,000 kg) resembles the
modern-day South American armadillo (2 kg).

36. Fossil evidence of evolution
Similarly modern Australia is filled with marsupials and fossils in Australia are of similar marsupial forms.
Extinct short-faced kangaroo.

37. Fossil evidence of evolution
Transitional forms
If fossil organisms are ancestral to modern organisms then there should be transitional fossils that show characteristics intermediate between the older and more recent groups.

38. Archaeopteryx
Archaeopteryx the oldest known fossil bird (name means “ancient wing) has mix of reptilian and avian features.
Reptilian: long tail, teeth, long clawed fingers
Avian: feathers, ribs with uncinate processes, avian shoulder girdle.

39. Archaeopteryx
(oldest known
fossil bird)
Jurassic
150mya

40. Evolution of mammals
There are numerous excellent fossil series that document the transitions from ancestral species to later species.
For example: the evolution of mammals from synapsid reptiles.
An extensive series of fossils documents the changes in the synapsid lower jaw from a jaw made of multiple bones to the modern mammals single dentary and the incorporation of some synapsid jaw bones into the inner ear.

43. Tiktaalik roseae
Another example is the evolution of the first amphibians from lobe finned fishes.
The transitional fossil Tiktaalik roseae possesses an intermediate suites of characters.
It has fish-like scales, palate and jaws, but an amphibian-like mobile neck and head, an ear that could hear in air, and the bones in its fins are intermediate between those of fish such as Eusthenopteron and Panderichthys and early amphibians such as Acanthostega.

44. Tiktaalik roseae 375 mya

46. http://images. google. com/imgres. imgurl=http://www. bringyou

47. Vestigial structures
Many organisms possess rudimentary or functionless versions of body parts that function in close relatives/ancestors.
The fact that structures are rudimentary implies they had ancestors in which these structures were functional. This suggests an evolutionary history.

48. Examples of Vestigial structures
Cave populations of Mexican tetra fish have eye sockets, but no eyes.
Kiwis have tiny, stubby wings
Boas have tiny remnant hind limbs

49. http://news. nationalgeographic. com/news/2006/02/images/060217_kiwi

50. Mexican Tetra

51. Human vestigial structures
Coccyx: vestigial tailbone at base of spine.
Arrector pili muscle at base of hair follicles makes hair stand up.
Appendix: reduced in size. Used in digestion of cellulose in herbivores e.g. rabbits.

52. Vestigial developmental traits
Adult chickens: three bones in forefoot (wing), four in hindfoot.
However, digit 5 appears briefly during embryonic development before disappearing.

53. Molecular vestigial traits
Human genome contains large numbers of pseudogenes that do not code for functional RNA or proteins. These are leftovers from evolutionary history once functional genes that have been turned off.
E.g. there are several pseudogenes of hemoglobin. May be as many as 6,000 pseudogenes in human genome.

54. Homologous structures
Homologous structures are those constructed from the same basic components which have been inherited from a common ancestor and then modified for different purposes.
E.g. The forelimbs of a human, mole, horse, dolphin and bat are constructed from the same bones, but the bones differ in size and shape and the structures made from the bones are used in radically different ways.

55. Homologous structures
Homologous structures make no sense if organisms were specially created, but they do if a set of organisms share a common ancestor and all inherited the same basic bone structure from that ancestor.
Homologous structures imply an evolutionary history and common ancestry.

56. Homologous structures (i. e. derived from a common ancestor)
Homologous structures (i.e. derived from a common ancestor). Even though the
forelimbs have evolved to carry out very different tasks they are all constructed
from the same bones.
FIG 2.11

57. Homology vs. Convergent Evolution
Not all similarities between different species are due to homology.
The streamlined shapes of sharks and whales are not a due to common ancestry but to convergent evolution.
The same selection pressures to be able to swim efficiently in water have independently produced similarly shaped bodies instead of the traits being inherited from a recent common ancestor.

58. Homology vs. Convergent Evolution
Whales and dolphins evolved from terrestrial ancestors about 50 million years ago, whereas shark fossils as much as 350 million years old are known.
The whales are most closely related to artiodactyls (hoofed mammals that include deer and hippos) and both whales and deer evolved from hoofed, carnivorous ancestors.

60.
killer-whale.jpg

61. Homologous vs. Analagous structures
Similarly, the wings of butterflies and birds are not homologous (because their structural components were not derived from a recent common ancestor) but perform the same function.
Such structures are analagous. They carry out the same function.

62. Molecular Homology
All organisms (with a few minor exceptions) use the same genetic code to specify which sequences of bases specify which amino acids when assembling proteins.
The reason the code is essentially universal is that a mutation that altered the code would alter almost every protein produced and so would be lethal.

63. Figure 1.1.1. The standard genetic code and known variant nuclear codes. 
(1) Candida, a unicellular yeast. (2) Micrococcus. (3) ciliated protozoans and green algae.
(4) Mycoplasma. (5) suppressor codon in bacteria. (6) Euplotes.
(7) the selenocysteine codon (8) Spiroplasma. (9) Micrococcus.
(10) resume codon in ssrA RNA (Lehman 2001).

64. Molecular Homology: Genetic flaws shared by different species
Chromosome 17 in humans PMP22 gene has duplicate sequence of DNA (CMT1A repeat) on either side of it.
It is the result of duplication and insertion of DNA and occasionally causes inaccurate crossing over during meiosis.

65. Molecular Homology
Humans share CMT1A repeat with bonobos and chimpanzees, but not gorillas, orang-utans or other primates.
Suggests CMT1A derived from common ancestor of bonobos, chimps and humans.

66. Atavistic traits
Atavistic traits are anatomical “throwbacks” that occasionally occur when a feature present in an ancestor reappears in a modern organism.
For example, occasionally horses are born that have additional toes either side of their hoof. Similarly, sometimes people are born with a short tail.

68. Atavistic traits
Such oddities are due to errors in development that cause ancestral traits normally suppressed in the genome to be expressed.
The presence of genes for such traits indicate an evolutionary history.

69. Atavistic traits
The embryos of a diverse array of vertebrates are very similar in early development.
Atavistic traits such as gill slits and a postanal tail, which are not present in the adult appear briefly before disappearing later in development.

71. Other evidence for evolution: jerry-rigged structures
Jerry-rigged structures e.g. the Panda’s thumb.
In pandas, a wrist bone has been modified into a “thumb” that is used to grip bamboo stalks and assist in stripping leaves.
The “thumb” is not a very efficient solution to the problem of bamboo stripping.

75. Panda’s Thumb Natural selection must work with the material
available to it. Process is more like someone
tinkering in their workshop and assembling an
object from spare parts than an engineer building a
structure from scratch.
The jerry-rigged nature of the panda’s “thumb” implies pandas were not designed, but evolved.

76. Other evidence for evolution: adaptive radiation
Adaptive radiation and clusters of species.
Many remote islands are populated by morphologically diverse clusters of closely related species.
This pattern is difficult to explain without evolution.

77. Process of adaptive radiation
Ancestral colonists arrive on island.
Shortage of resident species means many niches are unfilled.
Ancestral colonizing species gives rise to many species that occupy unfilled niches.

78. Adaptive radiation
Examples: Darwin’s finches on Galapagos Island, Drosophila on Hawaiian Islands.

79. Darwin’s Finches
On Galapagos Islands there are 13 species of anatomically very different, but closely related species of finch.
They differ greatly in beak size and diet having evolved very different lifestyles.

81. Hawaiian Drosophila
More than 25% of the world’s 1,250 species of Drosophila fruit flies found on Hawaiian Islands.
Few insect competitors so Drosophila have diversified to fill large number of niches.

83. If faunas were created why are there woodpecker finches, but no woodpeckers on the Galapagos Islands?

84. Artificial Selection
Artificial Selection. Humans as the agents of selection have selectively bred for desirable traits in domestic animals and plants for thousands of years.
The tremendous diversity of body forms that have been produced in domestic dogs in very few generations show how quickly organisms can change in response to selection.

85. Tameness in silver foxes
One excellent example of artificial selection is Dimitri Belyaev’s work to breed tame Silver foxes.
In each generation he bred only from the tamest individuals and in only six generations was able to produce foxes that were eager for human contact and behaved like domestic dogs rather than foxes.

86. Tameness in silver foxes
After about 30 generations 70-80% of the experimental population displayed extreme tameness.
In addition many foxes lots their fox-like look, became piebald and resembled Welsh collies. These were side-effects of selection for tameness (an example of pleiotropy: genes having more than one effect).

87. Silver fox after multiple generations of
selection for tameness (upper left)
content/42740/Belyaev_foxes_MED.jpg

88. Creationism and “Intelligent Design”
The idea of evolution has been harshly criticized by religious fundamentalists since the publication of the Origin in 1859.
This has been especially true in the U.S.
Repeatedly, believers in the literal truth of the Bible have attempted to have alternatives to evolution (i.e., creationism) taught in the public schools and to have the teaching of evolution either banned or restricted.

89. Creationism and “Intelligent Design”
The U.S. Supreme Court has prohibited the teaching of creationism in public schools as a violation of the establishment of religion clause of the Constitution.
Latest attempt to insert creationism into schools is the idea of “Intelligent Design.”

90. Creationism and “Intelligent Design”
The concept of “intelligent design” is outlined most clearly in Michael Behe’s book “Darwin’s Black Box.”
The central idea in “intelligent design” is that some structures in the body are so complex that they could not possibly have evolved by a gradual process of natural selection. These structures are said to “irreducibly complex.”

91. Creationism and “Intelligent Design”
By “irreducibly complex” Behe means that a complex structure cannot be broken down into components that are themselves functional and that the structure must have come into existence in its complete form.

92. Creationism and “Intelligent Design”
If structures are “irreducibly complex” Behe claims that they cannot have evolved. Thus, their existence implies they must have been created by a designer (i.e. God, although the designer is not explicitly referred to as such).

93. Creationism and “Intelligent Design”
Behe’s main examples are various biochemical pathways in the body, the blood clotting system, and structures such as the bacterial flagellum.

94. Creationism and “Intelligent Design”
Since the publication of Behe’s book, it has been demonstrated repeatedly that things he has claimed to be irreducibly complex are not in fact so.
E.g. the flagellum in eel sperm lacks several of the components found in other flagella, yet the flagellum functions well.

95. Creationism and “Intelligent Design”
The blood clotting system in dolphins lacks at least one component that the human system has, yet it too is functional.
In addition, plausible gradual scenarios for the evolution of biochemical pathways including the Kreb’s cycle have been documented.

96. Evolution of complex structures
The evolution of complex structures, such as the eye, appears difficult, but natural selection achieves this by the slow accumulation of minor improvements from one generation to the next.

97. Evolution of complex structures
Each step on the evolutionary pathway from a simple light sensing cell to a complex eye capable of focusing and producing color vision, must be beneficial to the organism that possess it and a slight improvement on earlier versions.
It is not necessary for a structure to be perfect or even very good, it just needs to be better than the alternatives to be favored by selection.

98. Variation in mollusc eyes from (a) pigment spot to (b) pigment cup to
(c) simple optic cup in abalone to (d) complex lensed eyes in a marine snail and
octopus.

99. Evolution of complex structures
Computer simulations suggest that eyes can evolve easily and in nature eyes have evolved independently more than 40 times.