CK-12 Biology I - Honors
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http://www.ama-assn.org/ama/pub/category/2306.html
http://www.americanheart.org/presenter.jhtml?identifier=4566
http://www.ift.org/cms/
http://www.pub.ac.za/projects/dnakits.html
http://www.fda.gov/cvm/CloningRA_FAQConsumers.htm
http://www.aavs.org/animalcloning_overview.html
http://www.FBI.gov
http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml
http://www.dna.gov/basics/analysishistory/
http://www.genome.gov/ELSI/
http://www.lbl.gov/Education/ELSI/
http://en.wikipedia.org/wiki/Main_Page
Vocabulary
CODIS
The Combined DNA Index System, is maintained by the Federal Bureau of Investigation and stores DNA profiles.
ELSI
Ethical, Legal and Social Issues. This term is associated with the Human Genome Project.
genetic fingerprinting (DNA fingerprinting)
Creates a unique DNA pattern that distinguishes between individuals of the same species using only samples of their DNA.
genetic testing
The direct examination of DNA sequences for mutated sequence.
microsatellites (short tandem repeats)
Adjacent repeating units of 2 - 10 bases in length, for example (GATC)n, where GATC is a tetranucleotide repeat and n refers to the number of repeats.
pharmacogenomics
The combination of pharmacology and genomics, is the study of the relationship between pharmaceuticals and genetics. It is the study of how the genetic inheritance of an individual affects his or her body’s response to drugs.
preimplantation genetic diagnosis (PGD)
Genetic analysis performed on embryos prior to implantation.
prenatal diagnosis (prenatal screening)
Testing for diseases or conditions in a fetus or embryo before it is born. Methods may involve amniocentesis or chorionic villus sampling to remove fetal cells.
restriction fragment length polymorphism (RFLP)
Analysis that analyzes the differences between restriction enzyme sites.
southern blot
Named after its inventor Edwin Southern, is a method used to check for the presence of a specific DNA sequence in a DNA sample.
STR profiling
Analyzes 13 STR loci to create a DNA profile utilized in forensic analysis.
transgenic animals
Animals that have incorporated a gene from another species into their genome.
transgenic crops
The result of placement of genes into plants to give the crop a beneficial trait.
Points to Consider
We have spent the past few chapters discussing genetics, molecular biology, and their implications. These are implicitly related to evolution.
Can you hypothesize on the relationship between genetics and evolution?
Why is an understanding of the principals of DNA and inheritance essential to understand evolution?
Chapter 11: History of Life
Lesson 11.1: Studying the History of Life
Lesson Objectives
Use the conditions required for fossilization to explain why fossils are rare.
List and give examples of different types of fossils.
Discuss the way in which index fossils contribute to our understanding of the history of life.
Compare relative dating of fossils and rock layers to absolute dating.
Explain why “carbon dating” is an inadequate description of aging rocks and fossils.
Describe how molecular clocks clarify evolutionary relationships.
Compare and contrast Geologic Time with absolute time. Include limits of each.
Sequence the levels of organization of the Geologic Time Scale from largest to smallest.
Arrange the four major Eons and one Supereon from youngest to oldest.
Describe and interpret the differences in fossil abundance throughout the Geologic Time Scale.
Distinguish macroevolution from microevolution and explain their relationship.
Describe the general pattern of the fossil record to support Darwin’s idea that all life descended from a common ancestor.
Evaluate the role of mass extinctions and episodic speciation in evolution.
Identify types of major environmental change in the earth’s history and relate them to patterns in the fossil record.
Analyze ways in which the Geologic Time Scale may give false impressions of the history of life.
Discuss rates of macroevolution and speciation, comparing and contrasting the ideas of gradualism, punctuated equilibrium and quantum evolution.
Compare and contrast adaptive radiation (divergent evolution) to convergent evolution.
Indicate some changes in geography which influence evolution.
Use patterns of evolution and environmental change to account for worldwide differences in the distribution of mammals (placentals vs. marsupials).
Define and give examples of coevolution.
Introduction
“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” - Charles Darwin, Origin of Species. 1859
The history of life as we currently understand it is vast and wondrous and dramatic and humbling and ennobling. Vast is the almost unimaginable expanse of time during which life has flourished: four billion years is our current best estimate! Wondrous is the diversity of species throughout that time: some 30 million species occupy Earth today, and over 90% of all which have ever lived are extinct. Dramatic are the tales of change in environment and in diversity: ice ages, volcanism, continental drift, mass extinction, and bursts of evolutionary creativity have all shaped the natural environment. Humbling is the recognition that humans have played a relatively small part in the history; if the 4.6 billion-year story of Earth is reduced to a single cosmological day, humans occupy just the last minute and a half, and civilization covers less than the final second (Figure below). Ennobling is the story’s revelation that we are related to and interdependent with all other species – back 4 billion years to “so simple a beginning” (Figure below). Finally, the history of life suggests we might add one more striking impression: Terrifying is the realization that we are in many ways unique among species in our unprecedented power to change the environment, influence evolution, and destroy life’s diversity.
If we as a species occupy just the last minute and one-half of the cosmological day, how can we know the vast history of that 4.6 billion-year “day?" How did we arrive at 4.6 billion years as the age of the earth? How we know is the topic of this first lesson on the history of life.
Figure 11.1
This Earth clock condenses the 4.5 billion years of earths history into a single 24-hour day. German names mark major geologic time periods. The last 17 seconds comprise the Quaternary period, spanning the past 2 million years. Human civilization appears only in the last second of the clocks 24 hours.
Figure 11.2
A family tree of living things summarizes our understanding of the history of life and shows that humans and animals share common ancestors with all of modern life. This diagram demonstrates our current understanding of evolutionary relationships. We will explore some of these relationships later in the chapter.
Tools: The Fossil Record, Aging the Ages, and Molecular Clocks
By age three, you probably knew that dinosaurs are part of the history of life. Our understanding of where they belong in the tale is relatively recent, but “dragon bones” have been known for thousands of years in China and Europe. Fossils are preserved remains or traces of organisms that provide extremely rare but vivid windows to the past. Because most parts of organisms decompose rapidly fo
llowing death, fossilization is an exceptionally uncommon occurrence, and usually preserves only hard body parts, shown in Figure below. Remains must be covered by sediment almost immediately. Buried organisms may experience mineralization (occasionally even within cells), or they may decay, leaving a space within the sediment later replaced with rock. Alternative pathways to fossilization include freezing, drying, trapping in resin (amber) or burial in anoxic (oxygen-free) environments. Trace fossils preserve footprints, burrows, droppings, eggs, nests, and other types of impressions. Overall, a great variety of types of fossils reveal the history of life, shown in Figure below.
Images in rock tell us what kinds of organisms lived in the past, but the story of life cannot be told without knowing when various organisms appeared. Paleontologists use two methods to date fossils. The oldest method looks at position within a sedimentary column of rock to give a fossil’s relative age. If the rock layers are undisturbed, the deepest layers are the oldest, and layers near the surface are the youngest, shown in Figure below. Widespread, short-lived index fossils can help identify rock layers of the same age spread around the earth, shown in Figure below. Combining worldwide observations of relative position and composition resulted in a Geologic Time Scale for the Earth – a column of rock layers which reflects the history of sedimentary rock formation and changing life, stretching back to a time which apparently held no life. The fossil record showed patterns which, combined with his observations of living species, led Charles Darwin to conclude that all life on Earth descended from a single, simple common ancestor.
Figure 11.3
was a small dinosaur from Early Cretaceous Italy. This fossil of a juvenile only a few inches long is considered one of the most important vertebrate fossils ever discovered, because unlike most, it preserved internal organs as well as hard structures. Fossilization of an organism is itself a very rare event; preservation of soft tissues is even less likely.
Figure 11.4
Different types of fossils reveal the history of life. Clockwise from top left: Amber preserves an insect intact. Stone etches impressions of Edmontosaurus skin. Rock echoes a dinosaurs footprint. Fossilized eggs recall a dinosaur of Mongolia. LaBrea Tar Pits fossilized the remains of a rich diversity of ice age animals. Permafrost preserved this female mammoth calf for nearly 10,000 years.
Figure 11.5
Relative aging dates sedimentary layers and the fossils they contain. Lower layers are older; upper layers are younger. Dinosaur fossils lie buried within this sedimentary formation in Green River, Utah.
Relative age, however, only begins the story. Absolute aging, also known as absolute dating, uses radioactive isotopes, whose known half-lives can be used to calculate the number of years which have elapsed since a rock formed. Radioactive decay is a random but exponential process. An isotope’s half life gives the time period over which half of the material will decay to a different, relatively stable product, shown in Figure below. The ratio of the original isotope to its decay product changes in a predictable way. This predictability allows the relative abundances of isotope and decay product to be used as a clock that measures the time from the incorporation of the isotope into a rock or a fossil to the present.
Figure 11.6
Single-celled algae serve as index fossils to correlate rock layers located in different states. The middle-aged rock layer in South Carolina has apparently eroded from a similar deposit of sedimentary rock in Virginia. Careful worldwide studies of relative age by many geologists and paleontologists led to the Geologic Time Scale.
Figure 11.7
Exponential decay of a radioactive isotope such as carbon-14 occurs with a unique, predictable half-life (t) of 5,370 years. The amount of carbon-14 remaining in a fossil organism thus indicates the time elapsed since death, giving a measure of absolute age.
For example, half of a sample of Carbon-14 will decay to Nitrogen in 5,370 years. Cosmic rays cause the formation of Carbon-14 from the more common and stable Carbon-12 at a relatively constant rate, so carbon dioxide in the atmosphere contains relatively constant, predictable amounts. Organisms acquire carbon from various mechanisms – plants from CO2, and animals and other heterotrophs through food chains. When an organism dies, its carbon intake stops, and existing Carbon-14 atoms decay exponentially, according to their 5,370-year half-life. The proportion of Carbon-14 in the organism’s remains indicates the time lapsed since its death.
Isotopes Used to Measure Absolute Age of Rocks and Fossils Isotope Decay Product Half-life Aging of Rocks or Fossils
Carbon-14 Nitrogen 5370 years Up to 60,000 years
Uranium 238/235 Thorium/Protactinium 80,000/34,300 years Hundreds of thousands of years
Potassium-40 Argon 1.3 billion years Earth’s oldest rocks
Uranium-238/235 Lead 4.5 billion /704 million years 1 million to > 4.5 billion years
Carbon-14 has a relatively short half-life, so its use for absolute dating is limited to a maximum of about 60,000 years. Other isotopes are used to reach deeper into geological time. Uranium-238 and Uranium-235 decay to different isotopes of lead with half-lives of 4.46 billion and 704 million years, respectively, and together allow dating of rocks between 1 million and over 4.5 billion years old. Table below shows some of the many isotopes can be used to study rocks throughout Earth’s 4.6 billion year history.
Absolute aging techniques confirmed and brought into focus the rock layer story geologists and paleontologists had developed with relative dating. They pushed Earth’s history back 4.6 billion years, and showed that complex life evolved after some two billion years in which bacteria alone populated the Earth.
Further confirmation of common ancestry included molecular clocks, which measure changes in DNA or proteins to indicate degrees of relationship among species. Comparing DNA sequences of several species of primates, for example, shows that chimpanzees are more closely related to humans than are gorillas or baboons, shown in Table below. If we assume uniform rates of mutation, we can estimate not only degree of relationship, but time back to common ancestry. Because DNA sequences (and mutations) determine the sequence of amino acids in proteins, Hemoglobin and other proteins are also used as “clocks.” Both DNA and protein clocks support a universal common ancestor for life, confirming the story which continues to unfold as new discoveries expand the fossil record. Molecular clocks, together with evidence from the fossil record, allows scientists to estimate how long ago various groups of organisms diverged evolutionarily from one another.
DNA “Clock” Comparison of Primates Species % Difference in Nucleotide Sequence, Compared to Humans
Human 0
Chimpanzee 1.2
Gorilla 1.6
Baboon 6.6
A Geologic Time Scale Measures the Evolution of Life
We noted in the previous section that observation of rock layers, dating techniques, and correlation of similar strata from around the world led to the development of a Geologic Time Scale (Figure below). How does the scale divide 4.6 billion years of history? What themes emerge from its stories of the past?
One theme is almost unimaginable amounts of time. The deep time of Earth’s history is far beyond our experience, and our knowledge is far more detailed for recent millennia than for the distant past. A scale divided into evenly spaced periods of time would not show that detail. Instead, Geologic Time Scale divisions mark major events which highlight changes in climate, geography, atmosphere, and life. The largest units of time are Eons. Eons include smaller Eras, which in turn include Periods, Epochs, and Stages. Faunal stages identify specific fossil groups. Terms such as Upper/Late and Lower/Early divide parts of the scale into more recent and more distant subunits.
Four eons comprise the history of Earth, and their names refer to a second major theme of Earth history: the evolution of life. The Phanerozoic (“visible life”) Eon spans the most recent 545 million years and includes three Eras well known for their chronicle of life: the oldest Paleozoic, middle Mesozoic, and curren
t Cenozoic. The Proterozoic (“before complex life”) Eon precedes the Phanerozoic, extending back 2.5 billion years. The Archean (“ancient”) and Hadean (“unseen”) Eons reach back to the formation of the Earth. The Precambrian Supereon combines the oldest three eons, and refers to the time before the first great explosion of life recorded in the fossil record - the Cambrian Period. The name “Cambrian” refers to Wales, where these fossils were first studied. Before this first period of the Phanerozoic, animals lacked hard body parts to contribute to the fossil record.
Figure 11.8
A linear arrangement of the Geologic Time Scale shows overall relationships between well-known time periods, which will be used in this and future chapters. Our knowledge of past life is concentrated in the most recent Eon, but the Phanerozoic occupies such a small proportion of the overall history of earth that eras, periods, and epochs are not precisely to scale. For future lessons, relevant parts of the scale will show more detail with greater accuracy.
Patterns and Processes of Macroevolution
Throughout geologic time, the fossil record reveals dramatic changes in species and groups of species which have populated the Earth. Evolution at or above the species level is macroevolution, in contrast to microevolution, which describes changes within a species or population. Many scientists no longer emphasize the distinction, believing evolution to be a single process which includes both patterns. However, themes from the Geologic Time Scale illustrate macroevolution, so we will consider its patterns and processes in this chapter.