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Biology 106

Biology 106 Spring 2012

Origins, Evolving Life Forms

and Ecology

Course Head: Dr. Peter C. Chabora

Photo by Steve Bloom from Nature 427:208, 15 Jan. 2004, doi:10.1038/42708a

Office hours: Tues. & Thurs. 3:00 - 4:00 pm

Office location: Colwin Hall, Room 104

I will be available for questions directly after the lecture in the lecture hall.

Biol 106: Spring 2012 Labs and Instructors

Mon. morning TBA 01-LEC (5372) Mon. afternoon TBA 02-LEC (5273) Mon. evening TBA 09-LEC (8705) Tues. morning TBA 03-LEC (5374) Tues. afternoon TBA 04-LEC (5375) Wed. morning TBA 08-LEC (5379) Wed. afternoon TBA 05-LEC (5376) Thurs. morning TBA 06-LEC (5377) Thurs. afternoon TBA 07-LEC (5378)

Morning labs: 9:15 am - 12:05 PM

Afternoon labs: 1:40 - 4:30 PM

Evening labs: 6:30 – 9:20 PM

Labs are held in Colwin Hall, Room 108

Biology 106 Laboratory Sessions 9th Edition

Sadava, David, H., David M. Hillis, Craig Heller and May Berenbaum. 2011. Life: The Science of Biology, 9th ed., Sinauer Associates and W.H. Freeman and Co., 1259 pp plus appendices.

Books and Manuals

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Books and Manuals

8th Edition

Sadava, David, H. Craig Heller, Gordon H. Orians, William K. Purves and David M. Hillis. 2008. Life: The Science of Biology, 8th ed., Sinauer Associates and W.H. Freeman and Co., 1245 pp. plus appendices.

Laboratory manual: Required for lab each week:

Chabora, Peter C., 2007. The Laboratory and Lecture Synthesis. Cengage, 400 pp.

Laboratory Manual

Biology 106 Blackboard

You are already registered into Blackboard for this course.

IMPORTANT: Be sure that you enter your current email address on Blackboard. It’s best to get used to using your @qc.cuny.edu address.

Also, use an email address that is sort of professional sounding – addresses such as HotLips@... or Superstud@... don’t really give a good impression.

Blackboard: Returned or Invalid Emails Invalid email addresses:

Returned emails:

Course Grading and Evaluation

Laboratory: total 40% of final grade •  Five quizzes = 2% each = 10% •  Two written reports at 5% each = 10% •  Laboratory manual evaluation = 5% •  Final practical examination = 10% •  Participation (on time, preparation, quality

of work, contribution to class, etc.) = 5%

Examinations: total 60% of final grade •  Two midterm exams = 20% each •  Final examination = 20%

A word of caution: Plagiarism and cheating are serious academic violations that will result in a failing course grade. Plagiarism may also result in visits with the Dean of Student’s Office, a notation on your record and possibly dismissal from the institution.

You are plagiarizing if you:

•  use or pass off as one’s own, the ideas or writings of another, or in other words,

•  appropriate as original to oneself the ideas or words of another, or in other words, cheating.

Do you get it? So, when using another individual’s ideas or writings, you must give credit to that individual by a proper citation.

This includes digital and electronic materials.

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The Scope of Our Studies: Hubble Images - 12 Billion Years - January 5, 2010

January 5, 2010: More than 12 billion years of cosmic history are shown in this unprecedented, panoramic, full-color view of thousands of galaxies in various stages of assembly.

A complete sphere is approximately 148,510,660,498 square arcminutes.

This is a square arcminute

The Andromeda galaxy (M31) with about a trillion (1012) stars.

This is the nearest major spiral galaxy to the Milky Way is the largest galaxy in the Local Group of Galaxies.

It is about 220,000 light years in diameter compared to the Milky Way's 100,000.

Photo: D. De Martin at the Palomar Observatory

So, here we are! A pale blue dot!

This photo of the Earth was taken by the spacecraft Voyager I on Feb. 13 or 14, 1990 from about 3.7 billion miles away.

That’s us - our home - not too significant are we?

But it’s a special place - to us.

Carl Sagan

Earth Life on Planet Earth

“The ecological theater for the evolutionary play”

G. E. Hutchinson, 1965

Think about the Earth and the characteristics of life as we know it. Temperature (20th century average = 54.1°F or 12.3°C) where water can be a liquid, solid, gas…..

…or life on Mars?

http://www.esa.int/esa-mmg/mmg.pl?topic=&subtopic=&keyword=Vastitas+borealis&subm2=GO

Gravity? Chemistry? Temperature? Radiation? History?

Falling Material Kicks Up Dust on Mar’s Dunes

There is a vast region of sand dunes at high northern latitudes on Mars. In the winter, a layer of carbon dioxide ice covers the dunes, and in the spring as the sun warms the ice it evaporates. This is a very active process, and sand dislodged from the crests of the dunes cascades down, forming dark streaks.

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How About Life on a Gas Giant Like Jupiter? Gravity? Temperature? Chemistry? Radiation? History?

http://solarviews.com/eng/jupiter.htm

…or, perhaps one of the moons of Jupiter, Europa, for example?

So How Do We Study Life on This Rather Curious Planet?

Life is an organized system, generated from transmitted molecular information and capable of metabolizing, reproducing and evolving.

…keep in mind… …that life, as we know it, arose and developed on Earth under various past and present conditions.

Important concept:

The characteristics and adaptations that we see in a species reflects the ecological and

evolutionary history of that species.

Five Organizing Concepts in Biology:

1.  Features of all organisms can be explained in physical and chemical terms.

2.  Organisms can be viewed as systems that take energy from their surroundings and convert it into biologically useful forms.

3. Molecular mechanisms encode and transmit information from one generation to the next.

Continued on next image

Five Organizing Concepts in Biology:

4. All organisms are composed of cells, the building blocks of life.

5. Through natural selection, organisms evolve adaptations to best fit their environment.

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“Nothing in biology makes sense except in the light of evolution.” Th. Dobzhansky, 1973

… so, what is evolution?

Evolution may be defined as a change in allele (gene) frequency.

Individuals cannot evolve but populations can.

Evolution is “the non-random survival of randomly varying hereditary instructions for building an embryo.”

Simply - “descent with modification”

Four general things to keep in mind in your study of biology:

1) Hierarchical structure of biological systems and the concept of emerging properties

2)   The importance of being familiar with the metric system and the manner by which conversions are made.

3)   The importance of understanding the surface area to volume ratio.

4)   The manner by which we examine the relationships between different kinds of living things.

The following seven images explore these concepts

The Hierarchical Organization of Biology…and What We Study in 106

The hierarchy ranges from the structure and function of atoms to the interactions of many kinds of organisms living in a given environment.

1. Atoms 7. Organisms

2. Molecules 8. Populations

3. Organelles 9. Communities

4. Cells 10. Ecosystems

5. Tissues 11. Biomes (regional ecosystems)

6. Organs 12. Biosphere

areas of concentration in Bio 106

Biological Hierarchy in

Levels of Organization:

Emergent Properties

Emergent Properties • Each level of biological organization has

EMERGENT PROPERTIES.

• These are properties not found at lower levels of organization and they do not violate principles that operate at lower levels.

For example, individuals are born and die, but they cannot show birth and death rates as do populations.

Or, consider the gaseous characteristics of elemental oxygen and hydrogen, then consider the characteristics of a molecule of water.

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Geometric Scaling in the Metric System Geometric Scaling in the Metric System

See Sadava et al., 2011, Fig. 5.1, p. 78.

Surface Area-to-Volume Ratio

See Sadava et al., 2011, Fig. 5.2, p. 78.

Tree of Life (Phylogenetic Tree)

See Sadava et al., 2011, Fig. 1.10, p. 12.

Some Light Energy is Captured by Living Things and Passed On to Other Creatures

Think about life and energy

Life and Energy Laws of Thermodynamics

First Law:

•  The total energy of the system remains constant, thus the energy in the universe is conserved.

•  Energy cannot be created or destroyed, but it can change form. Details of energy and its transformations is discussed in Chapter 8 of Sadava et al., 2011, Sec. 8.1, p. 148-53.

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Laws of Thermodynamics Second Law:

•  Entropy in the universe is always increasing.

•  Ordered systems become disordered (randomized).

•  Energy transformations are not 100% efficient and energy is lost at each transformation. Thus, entropy increases. There is no free lunch!

Entropy Without the input of energy to maintain order, entropy increases and objects become disordered (randomized).

Before and after pictures of Little Buffy.

Right, a highly organized Buffy, and below, Buffy becomes randomized and entropy increases.

Heat will not pass spontaneously from a body to a warmer one.

Sun’s Energy Passes Through Trophic Levels

Photosynthetic autotrophs capture sunlight and convert it into high energy compounds which are subsequently passed through the food webs.

Sunlight capture by producers is about 1% efficient – 99% is lost as entropy

Transfer of energy between trophic levels about 10% efficient – 90% is lost as entropy

Inorganic materials

Decomposers

Producers

Consumers

Energy Flux Through Biological Systems Energy is first concentrated, then dissipated, increasing the entropy of the system.

Energy flows through the system but atoms and molecules are recycled.

Input = Short wave radiation Output = Long wave radiation - increasing entropy

Life’s Energy Is Based on Excited Electrons Increasing the orbit of the electron increases the energy level of the atom.

This energy is harnessed by certain compounds and entered into life sustaining reactions.

Energy from the sunlight captured and raise the atom’s energy levels.

Sun’s Energy and Gravity Also Powers the Global Water Cycle

Driven by energy from the sun, water is a major cycling force powering with it the cycles of other elements and gases.

http://www.coexploration.org/howsthewater/html/earth.html

Water: Study Sadava et al., 2011, Sec. 2.4, p. 31-35.

Water cycle, Sadava et al., 2011, Fig, 58.8, p. 1229.

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: Basis of Life Raven and Johnson, 1996

The chemistry of living things is really the chemistry of carbon and water. Of all the molecules on Earth, water is one of the few that is liquid on the conditions of Earth and it is by far the most abundant. Between 60 – 97% of the weight of organisms is water.

Water: Structure, Polar Covalent and Hydrogen Bonds

Polar covalent bond H atoms are

at an angle of 104.5 degrees. WHY?

The symbol “δ” stands for charge, + or -

This represents a hydrogen bond; very important in water and biological systems.

Refer to Sadava et al., 2011, Fig. 2.11 -2.14, p. 29-31.

Note that the + and – charges on opposite sides of the molecule produce a dipolar molecule.

Note that the angle between the H atoms should be 104.5º in these “Bohr model” diagrams, not 90º as drawn.

Making Water Liquid: H-bonding

Electrons and the bonds are in continuous, extraordinarily rapid shifting, 1011 to 1012 times per second. Thus, the charge orientation and the H-bonding to other molecules is always changing – making water liquid and wet, rather than a gel!

At any moment an particular water molecule many have one of these four arrangements.

Beck et al., 1991

Hutchinson, 1957

Water Has the Highest Surface Tension

The water-air boundary has a strong tension due to the H-bonding of the water molecules among themselves.

Depression of the insect’s leg in the water surface.

Beck et al., 1991

Cohesion: Surface Tension This is an example of cohesion between water molecules.

Water molecules within the drop are H-bonded with each other producing surface tension the shape of the drop or bead.

Also, waxy surfaces are non-polar and do not permit water to form H-bonds, thus cohesion forms droplets.

Drops on a spider’s web

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Adhesion and Capillary Action Note that water will form H-bonds with some surfaces and not with others.

Water H-bonds with glass, so the smaller the diameter of the tube, less total surface to edge, the high water rises in the glass tube.

This is an example of adhesion, and is important in water going through the xylem in plants.

Where there is no H-bonding, there is no capillary movement – as with plastic.

Beck et al., 1991

Water: The Universal Solvent A crystal of table salt, sodium chloride (NaCl) placed in water ionizes; that is, it dissolves into charged particles of chloride (Cl-, which have a negative charge, and Na+ , with a positive charge). Hydration shells are formed with the positive ends of the water molecule facing the negative Cl- ions, and the negative ends of the water molecules facing the positive Na+ ions. Thus, the ions are kept in solution.

Raven and Johnson, 1996

Na+ ions attracting the – end of the water

molecule

Cl- ions attracting the + end of the water molecules

Keeping ions in

solutions

Covalently bonded NaCl

crystal

See Sadava et al., 2011, p. 29, Fig. 2.10

Thermal Properties of Water: Specific Heat

Definition: one calorie is the amount of heat energy necessary to raise the temperature of 1 gram of water (a volume = 1 ml or 1 cubic centimeter) from 14.5ºC to 15.5ºC.

It takes a lot of energy to heat water!

Beck et al., 1991

Thermal Properties of Water: Specific Heat of Evaporation

Large number of calories are necessary to turn liquid water in vapor. By evaporating water, we remove a great deal of heat. We regulate our body temperature by sweating.

Beck et al., 1991

Temperature and Water Density: So Important For Life on Earth

Ice at 0ºC (ice is 8.5% lighter than water at 0ºC).

From Wetzel, 1984

This is why ice floats – and our Earth is not a frozen planet!

Water is most dense at 3.94ºC.

Ice Structure

Note the distance between the H and O, and number of H atoms associated with each O atom.

The large amount of open space gives ice its lower density. Upper model is shown with correct shapes.

Lower model shows the geometry of the ice crystal lattice with the atoms drawn on a smaller scale.

Hutchinson, 1957

Interatomic distances affect water density.

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See Sadava et al., 2011, Fig. 58,5, p. 1226

Water Ionizes Only Slightly: Learning About Acids and Bases

Pure water at ordinary temperatures disassociates to free H+ and OH-

ions only slightly. 10-7 molecules per liter disassociate and we call this a pH of 7. This is neutrality because there is an equal; number of positive and negative ions. If the pH is lower (<10-7), the the solution is acid, if greater (>10-7 moles per liter) the solution is basic or more alkaline.

However, what is depicted in the above diagram does not happen in nature. H+ ions do not exist for long, but in fact combine as in the diagram on the right to form the hydronium ion.