ESCI 1st sem

Week 1: Introduction to Earth and Life Science

Origin and Structure of the Earth

The creation of the earth is thought to be directly linked with the creation of the sun. When the
sun was created, the cloud of dust and gasses that were left over formed the inside of the earth,
which stayed cool at 2000°F. As time passed, the elements in the solid center of the earth
started to decay. In the beginning the center of the earth was composed of iron and silicates,
along with materials that were radioactive. These radioactive materials, as they decayed,
emitted heat. Principally, these radioactive materials are composed of uranium, potassium, and
thorium. The heat that was released melted the silicates and iron. Since iron is heavier, it sank
towards the center. This became the core. Then, a layer of rock formed around the core. There
were depressions on the surface, and these are where water from the inside of the earth
accumulated.

Key Characteristics of the Earth's Structure

● Two magnetic fields in the earth which repels solar wind and protects the earth from solar
radiation
● Atmosphere of the earth is stratified, which means that it is made up of mainly nitrogen and
oxygen
● Earth is made up of a variety of minerals, melts, fluids, gasses, and volatiles, which were all
left behind after the solar system was created.
● The earth has layers: a crust, a mantle, and a metallic core The earth can be divided into an
outer lithosphere and a plastic asthenosphere.

The Subsystems of the Earth - Geosphere, hydrosphere, atmosphere, and biosphere.

- The atmosphere is the layer of air that surrounds the earth. It protects the earth from solar
rays. It also circulates the air and gasses that plants and animals need to survive.
- The biosphere is made up of living organisms, such as plants and animals. It is important to
note that all the biospheres interact with each other. For instance, plants and animals
(biosphere) interact with the atmosphere.
- The geosphere or also called the lithosphere, is made up of the physical earth, such as rocks,
magma, and soil. The geosphere extends from the center of the earth to the dust in the
atmosphere, and even includes the sand in the ocean.
- The hydrosphere, on the other hand, is made up of all the water held on earth. It includes the
water molecules in the air, icebergs and glaciers, lakes, rivers, groundwater, and oceans.
The Atmosphere - Divided into 6 layers according to altitude

● Exosphere: (500 km above the eath), this is where the atmosphere merges with space.
● Thermosphere: (90 km above the earth), this is where the space shuttles orbit.
● Mesosphere: (50-90 km above the eath), this is where meteors burn.
● Stratosphere: (12-50 km above the earth), this is where the air is stable and is good for planes
and jets to fly in.
● Tropopause: (11-12 km above the earth).
● Troposphere (0-11 km above the eath), the is the "mixing layer," all the weather is limited to
this layer.

The Geosphere

The crust is the outermost "skin" of the earth and has various thicknesses. The thickest is under
the mountain ranges, and the thinnest is under the mid-ocean ridges. The Mohorovicic
discontinuity or "Moho" is the lower boundary. It separates the crust from the upper mantle. It
was discovered in 1909 by Andrija Mohorovicio. It is also marked by a change in velocity of
seismic waves. There are two types of crust: the continental crust and the oceanic crust. The
crust is composed of just 8 elements. Oxygen is the most abundant element in the crust.
(Iron sank towards the center of the earth because it was heavy)

The mantle is a solid rock layer between the core and the crust It is composed of a rock called
peridotite It also convects: the cool mantle sinks and the hot mantle rises. Three subdivisions of the
mantle: upper, transitional, and lower The core is an “iron-rich sphere” with a radius of 3,471 km.
The outer core is made of liquid iron, nickel, and sulfur and it s 2,255 km thick. The flow in the outer
core creates the earth's magnetic field. The inner core is made of solid nickel, iron alloy It has a radius
of 1,220 km.

Formation of the Universe and Solar System - The universe and the solar system were formed about
4.6 billion years ago. However, scientists are not completely sure about how this happened. It is
important to understand this formation in order to understand how the universe functions and what we
need to know about it. (Universe is estimated to be 13.8 to 15 billion years old)

How the sun was formed:

1. There was a spinning disk in space.
2. As gas collected in the center of this spinning disk, a "protosun" was created.
3. Molecules in the protosun collided with each other, which caused heat to form.
4. This raised temperatures to 10,000,000°C. The heat and violent clashes between molecules
allowed the creation of nuclear reactions, which turned the protosun into a star.
How the planets were formed:

1. In the disk that surrounded the protosun, a process called accretion formed the planets, comets,
moons, and asteroids.
2. Small particles crashed together to form larger and larger particles, eventually reaching the size
of planetesimals, which are several kilometers big.
3. Since these planetesimals were big enough to have their own gravity, they caused even more
collisions around them.
4. In the planetesimals near the sun, the water evaporated and gasses were swept to the outside
and only the heavier materials could become solids. Young planets were formed from these
materials.
5. Farther away from the sun, the temperature was cooler. The amount of ice here allowed for
larger bodies to form, which created the core of the planets, such as Saturn and Jupiter.

Formation of the Universe:

The Big Bang Theory

Since the early part of the 1900s, one explanation about the birth of the universe has prevailed,
and this is the Big Bang Theory, Proponents of this theory have maintained that, between 13
billion and 15 billion years ago, all the matter found in the universe today was found in a
small space, a tiny contact point. Indeed, according to this theory, matter and energy were the
same back then. Adherents of the Big Bang Theory believed that, from this small but extremely
dense ball of matter/energy, expansion came about after an explosion. (Most popular theory)

Seconds after the explosion, the fireball that emerged ejected matter/energy at high velocities, which
approached the speed of light. At some time later, matter and energy separated from each other. All
the elements of the universe today developed from that original explosion. Moreover, proponents of the
Big Bang Theory believe that the explosive energy that was present back then is still retained today by
the stars and galaxies. The explosion back then still causes the expansion of the universe today, with
stars and galaxies moving farther and farther away from each other. The supposition of this movement
came in 1929 when the astronomer Edwin Hubble hypothesized that planets and stars are still moving
far away from each other, who was then conducting astronomical projects at the Mount Wilson
Observatory in California, announced that all of the galaxies that he was studying are moving further
and further away from us, at speeds that amount to several thousand miles per second.

The Steady State Theory

A competing hypothesis arose in the 1940s, in the form of the Steady State Theory. The
scientist who proposed this hypothesis was Fred Hoyle, who believed the universe was
governed by two principles: the cosmological principle and the perfect cosmological principle.
 The former is the idea that the universe is uniform in space, while the latter is the idea that the
universe is unchanging in time. Under this theory, stars and galaxies change, but the universe
remains the same as a whole.
The Steady State Theory also predicts that the universe is expanding, but it also predicts that new
matter is being created enough to fill the empty spaces left behind by the universe's expansion.
According to the Steady State Theory, matter cannot be created nor destroyed, but only transformed
into new forms- such as energy or as a different form of matter. Under this theory, the amount of new
matter formed is very small-one atom every billion years. This theory, however, fails in one significant
way: the average age of stars should be approximately the same if matter is continuously created
everywhere. This has been found to be false by astronomers.

The Plasma Universe

Individuals who do not subscribe to either the Big Bang Theory or the Steady State Theory are
formulating other views of the creation of the universe. Hannes Alfven, a Nobel laureate,
created a new model, since he is a plasma physicist. The theory first states that it has been
observed that 99% of the observable universe is made of plasma, which is where the term
Plasma Universe is derived from. Sometimes called the fourth state of matter, plasma is an
ionized gas that conducts electricity. The theory also discounts the Big Bang Theory and states
that the universe is crossed by electromagnetic fields and electric currents. Under this view,
the influence of an electromagnetic force has caused the universes to have existed forever.
Therefore, the universe has not beginning and no end. In the Plasma Universe, the galaxies take
as long as 100 billion years to come together. The evidence from the Plasma Universe does not
come from direct observations of the sky; rather they come from laboratory experiments.

The Earth's Internal Structure

The size of the earth is about 12,750 kilometers in diameter, and this was known by the
Ancient Greeks. However, it was not until the end of the 20" century that scientists were able
to be sure that the planet is made up of three layers: the crust, the mantle, and the core. The
crust, or the outer layer, is thinner than the mantle and the core. Underneath the oceans, the
crust varies in thickness, with a thickness of only just 5 km. The thickness of the crust that
exists underneath the continents is greater, which averages around 30 kilometers deep. Under
the larger mountain ranges, such as those under the Sierra Nevada or the Alps, the thickness
can extend up to 100 kilometers deep.

The crust of the earth is brittle and is liable to break. Below the crust, the mantle is found. It is a hot,
dense layer of semisolid rock. The mantle is approximately 2,900 kilometers deep. This layer of the
earth contains iron, calcium, and magnesium, and these exist in greater quantities than in the crust. The
mantle is also denser and hotter compared to the crust because matter is heated by the pressure and
temperature inside the earth. At the center of the earth is the core. The core is denser than the mantle
because it is composed of an iron-nickel alloy, which is metallic rather than being stony. The core is
made up of two distinct layers: the liquid outer core and a solid inner core. The liquid outer core is
2,200 kilometers thick, while the solid inner core is 1,250 kilometers thick.
As the earth rotates on its axis, the liquid outer core spins, which creates the earth's magnetic field.The
inner structure of the earth influences plate tectonics. The deep mantle is hotter compared to the upper
part of the mantle. These two layers of the mantle together form the lithosphere. Scientists believe that,
beneath this layer, exists the asthenosphere. The asthenosphere is composed of semi-solid, hot
material, which flows and softens after being subjected to high pressure and temperature. The
lithosphere is thought to be located above the asthenosphere, and the movement of the lithosphere
influences plate tectonics.

- Accretion: the process wherein particles are accumulated into a larger object.
- Nuclear reactions: the collision between two nuclei
- Planetesimal: an object that was created from rock, dust, and other materials.
- Plate tectonics: the theory that the outer shell of the earth is divided into several plates that
move over the mantle.
- Protosun: the ball of energy that preceded the sun; became the sun.
- Radioactive: the ability of the nucleus of an unstable atom to lose energy by producing
radiation
- Silicates: a salt whose anion contains both oxygen and silicon.
- Edward Hubble: stated the universe is still expanding in 1929
- Plasma: fourth state of matter
 Week 2: Earth Materials and Processes

Rocks and Minerals

Rocks are formed from distinct grains that come together. These distinct grains are called
mineral grains, and most rocks are commonly aggregates of these grains. Igneous rocks form
by crystallization (the mechanical deformation of rocks) and are usually composed of several
kinds of minerals. Sedimentary rocks, on the other hand, are composed usually of one kind of
mineral. This reflects processes in the rock cycle that favor the mineral's inclusion. Thus, the
assembly of minerals in rock is not at all random, but the result of the original rock-forming
processes.

Minerals are defined as: "a naturally occurring chemical element or compound, possessing a definite
crystalline structure based on an ordered internal arrangement of constituent atoms, and with a
chemical composition that may be expressed in terms of a unique chemical formula."

More than 2000 types of minerals are now known, and new ones are being discovered on a daily basis.
These minerals are classified according to chemical composition and atomic structure. However, the
majority of rocks are formed from one or more of a small group of minerals, just over a dozen. Silicate
minerals have a structure based on the silicate unit, which can be represented as part of a tetrahedral
building block. Six major groups of silicate minerals have been identified, based on the way that the
silicate units are joined together.Minerals make up rocks, and silicates crystallize in order to form
rocks. When tabulating the composition of minerals and rocks, it is common to denote the elements as
oxides, although these elements should not be taken to mean as oxides in the chemical sense. Each rock
is made up of one or more silicate minerals. Each rock, in addition to this, is made up of a distinctive
mineral composition. For instance, peridotites contain olivine and pyroxene. In contrast to this, olivine
is never found in granites. The main factor that determines whether a mineral is present after the
cooling process is the crystallization temperature. Each mineral is characterized by a different
crystallization temperature. It is now prudent to discuss the different types of rocks that are found on
the earth.

Igneous Rocks
Are the starting points in the rock cycle. That is, the materials that make up the other two types
of rocks, the sedimentary and metamorphic rocks, are derived from a source that is igneous.
Igneous rocks are found on the earth's mantle. It can be said that 70% of the earth's mass and
80% of the earth's volume consists of mantle rocks. Igneous rocks are derived from the
convection in the earth's mantle, and the source of heat energy for this convection is found in
the radioactive isotopes of potassium, uranium, and thorium. (mantle undergoes convection)

The types of rocks that contribute to the amount of energy in terms of heat energy per unit mass are
granites. Peridotites do not contribute much heat. Therefore, the former makes up much of the crustal
rocks. The internal heat of the earth may have come from the radioactive decay of potassium. One
obvious consequence of the heat in the earth's interior is the presence of volcanoes on the earth's
surface.
Volcanic rocks are products of volcanoes and they have three important characteristics:

1. they crystallize in the surface of the earth;

2. they are commonly fine-grained; and 3) they rest on top of older rocks rather than cut across
them. Volcanic rocks are an example of igneous rocks, which are formed from an exothermic
process. These rocks start out in the liquid state and then become solid.

Sedimentary Rocks
While igneous rocks are created from the cooling of magma, sedimentary rocks are classified as
secondary rocks because they come from igneous rocks. They are also secondary because they
come from the aggregation of pebbles and sand that have been compacted over time to form
rocks. In sedimentary rock, there are three types of grains: coarse, medium, and fine. These
grains are classified depending on the size of the grains.

Sedimentary rocks are also classified into three types: clastic, chemical, and organic (or biogenic).
Clastic rocks are basic sedimentary rocks and they have been created from "clasts" which are little
pieces of rocks that have been compacted and cemented to become larger pieces. On the other hand,
chemical rocks form when water evaporates. In other words, these rocks were created from chemical
precipitation. Lastly, organic rocks are rocks that contain shell fragments or fossils. Examples of
sedimentary rocks are: sandstone, shale, limestone, and conglomerate.

In response to environmental differences, the silicate minerals in igneous rocks undergo changes. These
changes lead to their total or partial breakdown. The process of breaking down is called weathering,
and it is this process that eventually results in the formation of sedimentary rocks. This is one part of
the rock cycle. There are two types of weathering: physical and chemical. Physical weathering is also
called mechanical disaggregation and chemical weathering is also known as chemical decomposition.
While physical weathering produces sedimentary rocks like sand, chemical weathering produces
residual minerals. In addition to this, sediments may be transported by wind, ice, and water.

Metamorphic Rocks
When rocks are subjected to mechanical forces as well as to extreme physical conditions, such
as temperature, they become metamorphic rocks. This group of rocks include all other types of
rocks, namely, igneous and sedimentary. Metamorphism occurs when the rocks are in the solid
state. The transition between metamorphic rocks and igneous rocks are marked by the melting
point of the rock. Below this melting temperature, the rock will become metamorphic.

The mechanical deformation of rocks concerns tectonic processes. The word tectonic means the
mechanical processes by which rocks are built up into complexities. There are two types of
metamorphism: contact metamorphism and regional metamorphism. The latter applies to large
sections of rock while the former applies to small sections of contact. Ex: slate, diamonds
Rocks that have broken or are weak undergo exogenic processes-erosion, transportation, and
deposition. A fragment of rock broken (weathered) from a larger mass will be removed from that mass
(eroded), moved (transported), and set down (deposited) in a new location. The weathering of rocks
usually occurs with the aid of geomorphic agents, such as ice, wind, and snow. Sometimes, however,
the only factor that causes weathering is gravity itself. For instance, rocks may slide down a slope due
to gravity, and this process is known as mass wasting. The rate of exogenic processes depend on
factors such as the resistance of rocks to erosion and weathering and the amount of relief and climate.

On the other hand, the endogenic processes or hypogene processes also occur, which uses heat from
within the earth.(are processes that occurred from inside the Earth.) In other words, when a process
originates from within the earth's crust, it is an endogenous process. These processes are governed by
the forces within the earth and are not very much affected by external sources. These processes also
cause phenomena such as earthquakes, volcanic activity, metamorphism, and the formation of ocean
troughs and continents. These processes are mostly caused by the thermal energy of the crust and the
mantle. The thermal energy in the mantle and the crust is derived from the decay of radioactive
material and the gravitational differentiation in the mantle. Earthquakes are a form of energy of wave
motion that is transmitted through the surface layers of the earth. It ranges from a faint tremor to a wild
motion. Earthquakes are due mostly to the dislocation of rocks underneath the surface. Tectonic
movements are movements of the tectonic plates. They may be folded, thrust over one another, or
broken up. Tectonic movements give rise to mountains, oceans, ridges, troughs, and other landforms.
When the process results in building up a surface, it is termed as diastrophism. Volcanism, on the other
hand, is the process by which matter is transported to the surface of the earth and then erupted.
Volcanism is the process wherein the magmatic materials are effused towards the surface of the earth
through volcanic structures. When the magma does not reach the surface, they are called intrusives or
plutons.

Plate tectonics is concerned with the movement of the continents. Proposed by Wegener, continental
drift is the theory that continents are moving. Continents are moving due to the movement of tectonic
plates on the earth's surface, or across the ocean bed. The evidence supporting continental drift is now
extensive. Along the shores of different continents, similar plant and animal fossils have been found,
suggesting that these continents were once joined together. One example is the fossil of the Mesosaurus,
which was found in both Brazil and Africa. Another form of evidence is that of paleomagnetism, which
is the process by which the magnetic fields of the earth move. Based on basaltic rocks, scientists at the
time did not know how to account for paleomagnetism. The magnetic field orientation of rooks of the
same age did not point to the same pole. The common magnetic north pole could only be established if
the continents were once in different positions than they are today. Using rocks with different ages,
they reconstructed the location of the continents during the past periods in geologic history. The
deformation of the earth's crust is the result of forces that are strong enough to move ocean sediments
to an elevation that is many thousands of meters above sea level. The deformation of rock involves
changes in the volume and/or shape of these substances. Changes in volume and shape occur when
strain and stress causes rocks to fold, buckle, or fracture. A fold is a bend in the rock that is the
response to compressive forces. On the other hand, a fault forms when the internal stresses in the rock
cause fractures. The fault can be defined as displacement of a rock that was once connected along a
fault plane.
History of the Earth

The magnetic field polarity of the earth changes. As a result, the magnetic field of the earth
shows normal and reversed polarity. The normal polarity is from the south pole to the north
pole, while reverse polarity is from the north pole to the south pole. The polarity changes are
key indicators of seafloor spreading. Seafloor spreading thus occurs in the ranges of the ocean
where volcanic activity gradually moves away from the ridge. This phenomenon helps explain
the continental drift in the plate tectonics theory. The divergence of the ocean plates causes
tensional stress, which in turn causes fractures to occur in the lithosphere. Then, basaltic
magma rises up from these fractures, and then this cools on the floor of the ocean and causes
the formation of new seafloor. New rocks will be found nearer the spreading zone, while older
rocks will be found farther away.

The oldest rocks in the earth include both the sediments, which are water-lain, and the ancient oceanic
crust. Thus, oceans have been forming ever since the beginning of the geologic period. From the
present oceans, no oceanic crust is known to be older than 180 Ma. The evolution of the ocean basin
starts from a rift, which then reaches a maximum size. It then shrinks and then closes completely.

Stages of Ocean Basin Evolution

1. Embryonic
2. Young
3. Mature
4. Declining
5. Terminal
6. Relict scar

Formation of Stratified Rocks and the Geologic Time Scale

The stratification of sedimentary and igneous rocks occurs on the Earth's surface. The layers
may be from several millimeters to several meters in thickness. These layers also vary much in
shape. Stratification planes are the names given to the separation between individual layers of
rocks. The stratification of rocks may occur due to the changes in composition or texture of the
rocks during deposition, or may also result from changes in deposition. Thus, a certain strata of
rocks may appear to be made of both fine and coarse particles. In the layers that have been
deformed, it is possible to make inferences about the geologic events that permitted these
events.
Thus, the history of the earth has been recorded in stratified rocks. The geologic time scale is the
temporal framework that is composed of the arrangement of stratified rocks. In order to find out the age
of the rocks, and thus the geologic time scale, geologists rely on two methods: relative and absolute
dating. The latter establishes how many years ago a certain event took place. The most important
aspect of absolute dating is based on the decay of radioactive elements in the rocks. On the other hand,
relative dating is able to place the events in their proper order, but cannot ascertain the exact number of
years ago when the event took place.

In order to date the rocks, marker fossils are used. Marker fossils, or index fossils, are able to indicate
the types of organisms that existed in a certain time period. They serve as guides to the age of the rocks
in which they are preserved. Since the geologic time scale is an important consideration when dating the
earth, it is also important for understanding the history of the earth. Organisms that only existed for a
certain period and found in rocks can determine the history of the evolution of organisms on earth.
Moreover, the earth's history in terms of animal and plant life can be deduced from the history found
within rocks by showing the time period in which they occurred.

- Basaltic rock: fine-grained, dark-colored igneous rock

- Basaltic magma: molten rocks that are rich in magnesium and iron, and lack silica
- Exogenic: coming from outside a system (geological processes that took place outside the
earth.)
- Endogenous: coming from inside a system
 Week 4: Natural Hazards, Mitigation, and Adaptation

Geologic Processes and Hazards

As was mentioned, the earth is a dynamic planet. The very forces that created the earth still act
at or beneath its surface. The movements of plates on the earth's surface, coupled with local
concentrations of heat, provide a continuing source of hazards for the people and the structures
that they build. Even with the present state of technology today, geologic hazards often cannot
be predicted or prevented with precision. The exception to this are landslides, which are
preventable.

Areas prone to such hazards can be identified through earthquake fault lines, coastal areas susceptible to
tsunamis, and areas near active volcanoes. Estimates of whether a certain hazard will occur are
probabilistic, because it is based on both the magnitude of the event as well as its occurrence in time
and space. Other measures, such as duration, speed of onset, geographical dispersion, and frequency
can be identified with even less precision. Nevertheless, appropriate measures for mitigating these
hazards can be taken.

Earthquakes and Landslides

Earthquakes are caused by strain energy underneath a fault line within the earth's crust. When
this strain energy is released, the result is an earthquake. There are three effects of earthquakes:
ground shaking, surface faulting, and earthquake-induced ground failure, which is composed
of landslides and liquefaction. Ground shaking, or ground motion, is the primary cause of the
partial or total collapse of structures on the earth's surface. It is the vibration of the ground
caused by seismic waves. Four types of seismic waves are propagated on the earth's surface
during an earthquake, each with different effects on structures. The sound wave, or P wave, is
the first wave to reach structures, and it causes buildings to vibrate. The second wave is the S
wave, which causes the earth to move at right angles towards the direction of the wave. It also
causes structures to move from side to side. Two low frequency waves also cause minor
vibrations. Buildings must be constructed to withstand these vibrations in order to prevent them
from being destroyed.

Surface faulting, on the other hand, is the tearing or offset of the ground surface caused by the
differential movement that occurs along a fault line. The effect of surface faulting is generally caused
by earthquakes that register as 5.5 or more on the Richter Scale. The displacemènt ranges from a few
millimeters to several meters. The damage caused by surface faulting increases with increasing
displacement. Buildings are susceptible to surface faulting, in addition to roads, bridges, railroads,
tunnels, and pipelines. The most effective way to prevent damage from surface faulting is to restrain
from construction along fault lines. Earthquake-induced ground failure occurs in a variety of forms.

Earthquake-induced landslides occur through a broad range of mechanisms. They occur in land that is
sloped steeply, and land that is flat. The principal criteria for classifying landslides are the types of
materials and the types of movement. The types of landslides that occur can be in the form of slides,
falls, flows, spreads, or a combination of these. On the other hand, liquefaction due to ground failure
can be classified into two types: rapid earth flow and earth lateral spreads. Rapid earth flows are the
most dangerous types of liquefaction. During this phenomenon, large masses of soil can move from a
few meters to a few kilometers. Earth lateral spreads are the movement of surface blocks brought about
by the liquefaction of subsurface layers. Liquefaction can be mitigated through appropriate engineering
design and ground-stabilization techniques. Human activities that trigger landslides include deforestation
and mining. The lack of trees allows water to flow freely down from the mountains in cases of rains
and storms. Water carries with it soil, which can engulf homes and other structures. The best way to
lessen the chances of a landslide in the community is to prevent the deforestation of forests.

Coping with Earthquakes

There are practical ways of coping with hazards brought about by earthquakes. One of these is
to build structures with construction standards that are compatible with the degree of ground
shaking. The second is to adopt ordinances that require investigating seismic sites and geologic
sites for hazards. Easements can also be established that are set apart from active fault lines.
Whenever an earthquake occurs, it is pertinent to stay away from electric lines, tall buildings,
and structures that may collapse. Trees should also be avoided.

Volcanic Eruptions

Volcanic eruptions are the spewing forth of lava from active volcanoes. They also consist of
tephra falls, ballistic projectiles, lahars, lava flows, and pyroclastic phenomena. Tephra falls
include rocks and blobs of lava that are ejected from within a volcano into the atmosphere.
These also form deposits as the debris falls back onto the surface of the earth. Tephra falls can
cause damage to structures and property due to the falling fragments. These fragments cause a
layer which covers the ground, and this produces a fine film of fine-grained particles in the air.
The accumulation of tephra causes buildings to collapse due to their weight. They can also kill
vegetation.

Pyroclastic phenomena, on the other hand, are masses of hot, dry pyroclastic material built into
masses. They are also hot gasses that move quickly along the ground surface. Lahars and floods are a
flowing slurry of volcanic debris and water that comes from within a volcano. The eruption of a
volcano that is covered in snow can melt enough snow that it will cause a lahar. Due to their high
density and velocity, lahars can destroy structures in their path. These include roads, bridges, crops,
and even whole towns.
This can then result in flooding when the water overflows from damaged dams and because of their
capacity to carry water. Volcanic eruptions can be mapped. These zones, which are typically located
within a certain radius of a volcano, will show areas which are susceptible to damage due to a volcanic
eruption. Called zonation maps, these maps can show the anticipated scales of future damage.The
mitigation of volcanic hazards primarily involves hazard assessment and land-use planning. There are
other mitigation practices, such as establishing monitoring and warning systems, protective measures,
evacuation measures, relief and rehabilitation programs, and insurance programs.
Hydrometeorological Phenomena and Hazards

Floods - One of the most common hydrometeorological hazards is flooding. They are common and
very costly for the community. Conditions that may cause flooding include rains that last for several
days and water that seeps into the ground. Flash floods, on the other hand, occur due to the sudden
overflowing of rivers along a stream or a low-lying area. There are several types of floods: flash
floods, river floods, coastal floods, urban floods, ice jams, and glacial lake outburst flood. The
characteristics of floods vary. First, the depth of water brought about by the flood will have different
effects on buildings and vegetation.Secondly, the duration of floods will determine the damage to
structures. The velocity of the flood may create erosive forces, especially if the velocity is high.
Hydrodynamic pressures caused by the velocity of the water, and these destroy foundations of
construction or agricultural activities. The frequency of occurrence is measured over a period of time.
Seasonality, on the other hand, is when the floods are most likely to strike, and can have devastating
effects on crops and structures.

Flood preparedness and mitigation have been around for centuries. The first way to mitigate the effects
of floods is to properly regulate and enforce rules related to developmental activities. These activities
are primarily located near floodplains of rivers. Encroachments to water flows in rivers are also causes
of floods, and should be regulated as well. Effective steps are needed to regulate unplanned growth in
the flood plains. Capacity development is composed of flood education. These activities target groups
for development. They also include developing the capacity of individuals, such as professional
training, research, and development with respect to the management of floods. Flood response is an
effective measure to prevent the large loss of lives associated with rising water levels. There should be
evacuation measures, as well as warning signs that will mitigate floods. There are also structural
measures, such as the construction of embankments that are designed to minimize the effects of floods.
Dams, reservoirs, and other mechanisms for storage of water are also effective means to contain floods.
Desilting and dredging of rivers is another approach to minimize the effects of flooding.
Cyclones - The tropical cyclone is another phenomenon that occurs within the earth's atmosphere.
Cyclones are termed as such when their winds equal or exceed "gale force," which is a minimum of 62
kmph. These are intense areas of the earth's atmosphere that coincide with system and extreme weather
events. A cyclone is characterized by a center that is large and of low pressure. It also has numerous
thunderstorms that produce flooding rain and strong winds. When moist air rises, cyclones feed on the
air, which results in the condensation of water vapor in the moist air. The term "tropical" refers to the
geographic origin of these systems, since they form almost exclusively in certain parts of the globe. The
term "cyclone" on the other hand, refers to their counter-clockwise movement from the Northern
Hemisphere, and the clockwise rotation in the Southern Hemisphere. Depending on its strength, a
cyclone may be termed as a hurricane, tropical storm, tropical depression, cyclonic storm, or simply
cyclone.

Cyclones, aside from producing heavy rains and winds, can also produce high waves and storm surges
which are damaging. These phenomena develop over large bodies of water, subsequently losing their
strength as they move over land. Thus, coastal regions receive much of the damage from cyclones,
while regions inland are safe from their effects. Although they have devastating effects on people and
structures, cyclones are also helpful in maintaining the earth's troposphere, maintaining a relatively
stable and warm temperature worldwide. Cyclones are known to cause severe damage due to strong
winds. These winds damage installations, buildings, houses, and communication systems. This results
in the loss of property and life. On the other hand, torrential flooding and inland flooding, also cause
major damages. Torrential rains are those that fall more than 30cm/hour. Rain is a serious hazard that
is caused by cyclones, as people lose shelter due to it. A storm surge is an abnormal rise of sea water
near coastal areas and is caused by a severe cyclone. In order to avoid damages due to cyclones,
individuals must listen to weather reports regularly. Safe shelters in an area must be identified. These
are shelters where people can evacuate to in cases of extreme destruction. Remaining indoors while the
cyclone is active is another safety measure. Emergency kits must also be acquired, which contain first
aid for wounds, and enough supplies to last until the cyclone is over.

Tornadoes - Tornadoes are rotary storms that appear as a whirling and advancing funnel of wind
extending downward from a cloud. Tornadoes can occur in any part of the world. They are, however,
uncommon in the Arctic region, since no cumulo-nimbus clouds are formed there. They are also not
likely to occur in the equatorial zone because the cumulonimbus clouds in these areas do not have all
the characteristics that are needed to form tornadoes. The region that is most frequently hit by
tornadoes is the Midwestern United States, from Texas to Iowa. These areas are sometimes termed as
"Tornado Alley." Tornadoes are also very small as compared to cyclones. They are rarely more than a
few hundred meters in diameter. However, they sometimes reach 3 km in diameter. The lifespan of a
tornado is usually not more than a few hours. (Most destructive type of natural hazard)

The velocity of the wind during a tornado can be very high, and the strongest wind ever recorded is
observed in Texas in 1958, where the velocity reached 125 m/s. Additionally, the high destructive force
of a tornado is conditioned by a sharp difference in pressure between the center of the vortex and the
circumference of the tornado. While a tornado is passing, the air pressure can suddenly drop by 100-
200 hPa in a span of a few minutes. This may cause buildings to explode because of the difference in
air pressure inside the enclosed space and outside it. Hail, or the ice, is another consequence produced
by a tornado. The total impact of a tornado surpasses all other natural disasters in terms of the
destruction caused. Due to the unpredictable nature of tornadoes, only a general forecast can be
created. Tornado warnings on a particular day when a tornado is imminent are usually very inaccurate.
Safety measures during tornadoes include creating an emergency supply kit, with food, water, and first
aid materials. Taking shelter indoors should be done when a tornado is approaching. Avoid windows,
and protection should be sought by getting underneath furniture that is large and solid. Mobile homes
and automobiles should also be avoided. Those that are caught outside should lie flat on the ground and
wait for the tornado to pass.

Coastal areas, which are boundaries between water and land, are characterized both by the dynamic
power of the sea and the wind, and by the geologic nature of land, which is fragile and often unstable.
As a result of this dual nature, coastal areas are constantly changing as they are struggling to maintain
an equilibrium between many naturally opposing forces. The risks of living in coastal areas are
primarily for those who are living near an earthquake fault, river floodplain, or near a volcano. Since
coastal areas are attractive places to live in, the natural equilibrium of these areas are further disturbed,
which has led to a coastal crisis. Coastal erosion affects about 90% of the world's coasts and occurs at
varying rates. Coastal erosion gives rise to increased storm activity and rising sea levels.

There are five main processes by which coastal erosion occurs: corrasion, abrasion, hydraulic action,
attrition, and corrosion/solution. Corrasion is when the waves acquire materials from the beach and
then hurl them at the base of a cliff. On the other hand, abrasion occurs when waves, which contain
sand and other fragments, erode the headland or the shoreline. This is also known as the "sandpaper
effect." Hydraulic action is when the waves hit the base of a cliff, subsequently compressing them into
cracks. Attrition is when the waves cause rocks and pebbles to collide with each other and break up.
Corrosion is when the cliff eroes as a result of the acids in the sea. Submersion, on the other hand, is
the portion of coastal erosion which is sustainable. This occurs when rocks and other sediments move
from the beach's visible portion to the nearshore region which is submerged. The reverse of this
process, which is the recovery process, is known as accretion.
Saltwater intrusion is the movement of salt water, or saline water, into freshwater aquifers. This can
lead to the contamination of drinking water and other consequences. Saltwater intrusion can occur
naturally, to some degree, in the majority of coastal aquifers. This is due to the hydraulic connection
between seawater and groundwater. Human activities, such as groundwater pumping from freshwater
wells in coastal areas, can increase saltwater intrusion.

Tides - The moon and the sun have gravitational pulls on the ocean, which create oscillations called
tides. As the earth spins, the position of the moon overhead sweeps across all the latitudes. The gravity
from the moon, when it is overhead, produces a high tide. This may also happen on the opposite side of
the earth at the same time as water is "pulled away" from the sides of the planet, and this is where low
tides occur. In every 24-hour period, there are two low tides and two high tides. When the sun and
moon are lined up together, and the moon is closest to the earth, the high tides are maximum (spring
tides). When the moon and the sun are at 90 degrees from each other with regards to the position of the
earth, then the low tides are at their minimum (neap tides).

Waves - Waves are considered to be disturbances in the water caused by the water energy that is
passing through the water. In open ocean basins, the source of this energy is wind. The energy from
the wind is transferred to the water as wind blows across it. The waves' characteristics are

geometrically described. These are:

1. the amplitude or the wave height;
2. the wave length;
3. 3) the wave period.

The wave height is the vertical distance between the top of the wave and its trough. The wave length
refers to the horizontal distance between successive troughs or crests of the wave. The wave period
refers to the number of waves that occur in a given period of time. Overall, these characteristics are
determined by the duration of the time that the wind is blowing, the wind speed, and the "fetch,"or the
distance across the open sea that the wind has traveled. The wave's height and its steepness vary
according to the amount of energy that the wind transfers to it.
Sea-Level Changes - Sea-level changes typically occur as a result of increases in water temperature,
which increases its volume. The effect of sea-level changes can be local or global. They are local when
the water mass is relatively contained, and they are global if a large portion of the ocean's water mass
is impacted by warming. Conversely, as the temperature of the seas goes down, this results in
reductions of sea water volume, giving rise to lower sea levels. Mathematicians and geoscientists have
tried to theorize models that cause sea level changes, but so far no one theory is able to explain the
whole phenomenon. However, what is certain is that a rise in temperature causes the sea level to rise
owing to changes in the volume of the sea water. The effect of a small rise in temperature can
extrapolate to changes in sea levels over the entire globe. This extrapolation, when considered over
time, can produce large increases in sea levels. As such, scientists believe that the recent rise in sea
level is caused by global warming.

Crustal Movements - The real cause of crustal activity can be ascertained from the movement of the
crust and the crustal structure. However, there are very few studies that refer to the relationship
between crustal movement and crustal structure. Real-time observations of the crustal movement have
been generated by observations by geologists. The evidence for crustal movement, which is the most
obvious, are earthquakes. During an earthquake, the movement of the crust occurs along the faults.
Volcanic eruptions also involve movements of the crust, as do displaced structures. Bench marks are
metal plaques set in the soil that give the exact locations of the elevation points. These marks are used
as reference points in geological surveys and measurements of elevations of bench marks reveal that
large areas of land are moving upward or downward. The causes of crustal movement include the
action of unbalanced forces acting on the earth's surface. These forces include gravity, the expansion
and contraction of rocks, the forces produced by the rotation of the earth, and by the density currents
found in the mantle of the earth. These many forces are called stress. On the other hand, tension pulls
the rock into two different directions, causing it to break apart or stretching it. Compression consists of
forces acting towards each other, which pushes or squeezes rocks together. Finally, shear stresses may
act away or toward each other, causing the rock to twist and tear.
 Week 5: Introduction to Life Science

The Historical Development of the Concept of Life

There are two biographies of life. The first is ontogenic, synthetic, and developmental. This is
based on the properties of cells and their ecological (bio geomechanical) consequences. The
second is the historical-collective, populational, diachronic, and evolutionary process. The two
main pillars that sustain life are metabolism and genetics. Each living thing on earth uses
external sources of energy to fight the disorder and to maintain equilibrium. Organisms also use
external energy sources in order to fight against death. Molecular machines and membranes are
located as part of the frontier between inside and outside. They also manage flows of energy
and matter that would benefit the cell. In current life forms, these mechanisms are dependent on
digital genetic records. The change, acquisition, and loss of fragments of information from cells
underlie the evolutionary process. The historical persistence of these records of genes is
absolutely dependent on the ecological and metabolic abilities of organisms. Thus, the
fundamental question emerges: how did life come to be on earth? Which came first, the
hereditary properties of living matter or their autopoietic properties?

What is Life?

The definition of what constitutes life is a hard question. However, life can be loosely defined
as a living being is any autonomous system with open-ended evolutionary capacities." The term
autonomy refers to the organism's relationship with its environment, as well as the mutal
modifications of both, as well as the capacity of the organism to use matter and energy to create
its own components. This means that living things can self-construct, through which they are
able to build an identity that is separate from the environment. In the simplest case, a living
organism is a cell. On the other hand, the term "open-ended evolution" refers to the capacity of
living things to explore novel functions and relationships with their surroundings, including
other living things. It also pertains to their ability to adapt to situations in a way that is almost
unlimited.

There is a range of physical conditions that are compatible with life. Wherever there is an energy
source that can be used (visible-light protons, certain chemical reactions that are inorganic, or organic
matter), as well as liquid water, biological activity can be found. At a molecular level, living organisms
also show a striking biochemical unity. The same basic cellular organization, the repeated use of
genetic matter in the form of DNA, the genetic code that is universal, and the variations that are found
in the same bioenergetics mechanisms (i.e. chemiosmotic energy currency and chemical currency).
Thus, the explanation for all these suppositions on terrestrial life is that they come from a common
ancestor, which was observed by Charles Darwin.
The Origin of Life

How should the study of the primordial steps of the evolution of life proceed? Using a top-down
strategy, all organisms that are known are compared in order for the reconstruction of the
metabolic and genetic makeup of the universal "cenancestor" proposed by Darwin. Thus, in
the universal sense, there are two branches to the tree of life. These are the bacteria and the
Archaea. The Eukarya domain is considered to originate from prokaryotic partners, and is a
chimera. On the other hand, the bottom-up approach starts with planetary, cosmological, and
geological information, as well as information from other sources that can be used to
reconstruct the ambient, which are the chemical inventories and processes that are involved in
the origin of life.

In the 1920s, Aleksan dr I. Oparin fathered the notion that the origin of life has unfolded based on the
physicochemical processes that occur on earth. However, the importance of Oparin's theories are not in
the facts that he presented, but rather on the intellectual idea that historical hypotheses can be tested,
and even simple artificial life forms created. For instance, in 1953, the Urey-Miller experiment became
the start of the prebiotic chemistry program. Since then, many chemical reactions, such as the synthesis
of amino acids and nucleic acid bases, have been proposed. The Urey-Miller experiment provided
experimental evidence for Oparin's theory. Oparin's theory is popularly known as the "primordial soup
theory," referring to the aquatic origins of organisms.

The following steps comprise the Oparin's theory:

1. The atmosphere of the early earth was chemically-reducing.

2. This type of atmosphere, which was exposed to various forms of energy, was able to produce
simple organic compounds (monomers).
3. These compounds accumulated in a "soup" which may have been accumulated in various
locations.
4. Through further transformation, the more complex organic compounds (polymers), and
ultimately, life, developed.

Following the scenario proposed by Oparin, prebiotic organic molecules, which may either be
terrestrial or extraterrestrial in origin, were built up from the oceans. This promoted the proliferation of
organisms that can survive in aerobic environments. In this scenario, then, life started as heterotrophic
and anoxygenic cells. On the other hand, Gunter Wachtershauser proposed that the origin of life was
both autotrophic and thermophilic. He suggested that pyrite was the energy source, as well as the
electron source, of all living matter. Although his theory may be viable, evidence is still lacking as to
the autotrophic origins of life. That being said, there are several standpoints that have been debated
upon concerning the origin of life.
Heterotrophic vs. Autotrophic Origin - The standpoint in this case is that either life started out as a
simple system that took advantage of the environment, as proposed by Oparin, or self-sustained systems
emerged early on, as proposed by Wachtershauser. Upon considering the chart of the autotrophic
evolution, then Oparin's theory is more plausible, as conferred by experts.

Replicators or Metabolism First - The principal debate here is whether genes, or genetic material,
emerged first (as proposed by Henry Muller), or whether proteins emerged first (as proposed by
Leonard Troland). Many authors believe that the origin of life emerged as the first replicators, or the
first molecules that copied themselves. There are several supporting experiments that gave rise to
evidence that genetic materials came

first. One of these experiments was created by Tom Cech and Sydney Altman, who discovered catalytic
RNA. Catalytic RNA causes the formation of proteins from genetic materials. However, those that
contest the replicators theory contest that there is no way to efficiently use energy without the necessary
proteins. Thus, several researchers, including Wachtershauser, have advocated for the emergence of
primitive, self-catalytic metabolic networks as the primary step towards the creation or synthesis of
replicators. Those prebiotic processes, which are self-organized, would have provided a useful
scaffolding for the emergence of genetics.

Early or Late Cellularization - The debate surrounding the origin of life includes whether the
formation of compartments was a late or early phenomenon. This debate is closely related to the debate
between whether genetic material or proteins came first. Those that regard the early emergence of
replicators have regarded the cell as physical compartment in which polymers are segregated. However,
ample evidence from biochemistry has shown that the cells is not simply a compartment that is enclosed
by a semi-permeable membrane. Instead, the cell's interior is a physically and chemically different
environment from the outside because of the presence of active phospholipid membranes and their
protein machines. Thus, the essence of bioenergetics lies in the disposition, which is asymmetric, or the
molecular machines on the membranes of cells and the corresponding chemical messengers allowing
coupling between energy sources and metabolic networks. It is worth noting that this debate has spurred
the bottom-up strategy for the chemical synthesis of life.

Unifying Themes in the Study of Life - The study of life is rife with themes that are common to all
living things. These themes are important for characterizing what living things are, and can help in the
study of their origins as well as their characteristics. Evolution is the mechanism by which an organism
adapts to its environment. Biology is the scientific study of life. Life is recognized through a set of
characteristics.
Theme 1: New Properties Emerge at Successive Levels of Biological Organization

The study of life can be as great as on a global scale, to as small as the study of cellular
organisms. Reductionism is the approach of breaking down complex systems into simpler
systems that are more manageable for study. For instance, the molecular structure of DNA can
be broken down in order to understand the chemical basis of inheritance.

Emergent Properties are properties that are new, and that emerge at each level of organization. These
properties are absent from the preceding level. Systems biology is a system that combines components
that function together. This type of biology attempts to model the dynamic behavior of the whole
biological system, which is based on the study of the interactions between the parts of the system.
Structure and Function is a major theme in biology. That is, the organism's form must fit its function.
For instance, a hummingbird's wings are designed to beat rapidly and to set it to fly. Analyzing the
structure of organisms gives clues as to how it works. Conversely, analyzing its function can give rise
to clues about how it is constructed.

The Cell is the basic unit of life structure and function. This is the lowest level of biological
organization and can perform all the activities required for it to survive. Understanding how cells work
is a major focus of research endeavors in biology. There are two main cell types: eukaryotic and
prokaryotic. Eukaryotic cells contain organelles in their cytoplasm. Prokaryotic cells, on the other
hand, are simpler cells and do not contain organelles in their cytoplasms.

Theme 2: Life's Processes Involve the Expression and Transmission of Genetic information

The division of cells to form new cells is the basic foundation for the growth and reproduction
of all organisms. In the dividing cell, deoxyribonucleic acid is short for (DNA) is replicated
and then partitioned between two resulting daughter cells.

DNA is where genes are found. Genes are the basic units of inheritance that transmits the genetic
information from parents to offsprings. DNA controls the development and maintenance of the whole
organism. It is also responsible, albeit indirectly, for everything that the organism does. DNA is the
storage space for genetic information and a polymer. It is composed of nucleic acids, which are
building blocks for genes. These nucleic acids are: guanine (G), adenine (A), thymine (T), and
cytosine (C).
DNA also controls the production of proteins through an intermediate molecule. This intermediate
molecule is known as ribonucleic acid (RNA). The process of transcribing genetic information to
proteins is

known as gene expression. However, not all RNA are transcribed into proteins.
Genomics is the large-scale study of DNA sequences. The entire "library" of genes in an organism is
termed as its genome. The new area of genomics is concerned with studying the whole sets of genes of
a species. Proteomics, on the other hand, is the study of proteins and their properties.

Theme 3: Life Requires the Transmission and Transformation of Energy and Matter

A fundamental characteristic of all living things is that they use energy to carry out their
activities, and to sustain them. Growing and moving requires work, and this work requires
energy. Living organisms function to transform the types of enegery. For instance, solar energy
is transformed to chemical energy (sugar) through the process of photosynthesis. The flow of
energy in living things starts with producers (plants) to consumers (animals), and then to
decomposition (bacteria and fungi).

Theme 4: From Ecosystems to Molecules, Interactions are Important in Biological Systems

Ecosystem encompasses an organism's interaction with the physical environment and other organisms.
At the level of the ecosystem, each organism interacts with other organisms. In addition to this,
organisms also interact with other factors of the physical environment.

Molecules interact with organisms. The regulation of biological processes is important for the operation
of living systems. The chemical processes of the cells are mediated by active proteins called enzymes.
The chemical pathway contains several steps, and each step is controlled by an enzyme. Biological
processes regulate themselves through a mechanism called feedback regulation. Negative feedback
occurs when the accumulation of the end product halts the chemical process. On the other hand,
positive feedback occurs when the product speeds up its own production.

Theme 5: Evolution is the Core Theme of Biology

Organisms exhibit the diversity as well as the unity of evolution. Living organisms have shared traits
(unity). Yet, each organism is suited to its own environment (diversity). All organisms are descended
from a common ancestor. Charles Darwin proposed the theory of evolution, after observing animals
from his boat, the SS Beagle.

- Anoxygenic: does not use oxygen

- Autotrophic: an organism that is capable of synthesizing its own food using light or chemical
energy / refer to organisms that are using energy from sunlight or inorganic compounds to
produce organic compounds.
- Bioenergetics: the study of transformation of energy in all living things
- Chemiosmotic energy: energy derived from the movement of ions across a selectively
permeable membrane
- Diachronic: concemed with the development of an organism, or language.
 - Heterotrophic: Organisms that use energy from sunlight or in organic compounds to produce
organic compounds
- Polymers: repeating units of monomers
- Thermophilic: drawn towards heat
- Ontogenetic: concerned with the origin and development of an organism.

Week 7: Biogenetics

The Cell as the Basic Unit of Life

The cell is the basic unit of life. Organisms may either be unicellular (composed of one cell
alone), or multicellular. Cells comprise both animals and plants, although there are differences
with regards to each. However, the cell is the smallest unit of life. Cells may come together to
form tissues, which can come together to form organs. Organs make up the human body, as
well as the bodies of plants and animals.

The study of the cell is not possible without a microscope. Anton van Leewenhoek constructed the first
simple microscope. He was able to study the structure of bacteria, protozoa, spermatozoa, and red
blood cells. Robert Hooke, in 1665, coined the term "cell" that he used to designate the small, honey-
comb like structures that he was able to view on a cork bottle. He was impressed with the little
structures, as they reminded him of rooms in a monastery. In 1838, Matthios Schleiden proposed that
all plants are made up of cells. Then, 1839, Theodore Schwann proposed that all animals were also
made up of cells. Together, Schleiden and Schwann studied a wide variety of plant and animal tissues,
and proposed the Cell Theory in 1839. The theory essentially stated that all organisms are made up of
cells. However, the theory was rewritten by Rudolf Virchow in 1858. In the succeeding theory,
Virchow wrote that, aside from all living things being made up of cells, all cells arise from pre-
existing cells. In 1861, Schulze found that cells were not empty, as Hooke thought, but that they
contained material known as protoplasm.

It was during the 1950s that scientists were able to classify cells according to eukaryotic cells and
prokaryotic cells; with the latter lacking a nucleus. Another important difference between prokaryotes
and eukaryotes is that prokaryotic cells do not have any intracellular components. Prokaryotic cells
include bacteria and blue-green algae, while eukaryotic cells include plants, animals, fungi, and
protozoa. (eukaryotic cells lack a nucleus)

Modem Cell Theory - Biologists today have made additions to the cell theory, which now states:

1. All organisms are made up of cells;

2. New cells arise from pre-existing cells;
3. The cell is the structural and functional unit of all living things;
4. The cell contains genetic information that is passed from cell to ceH during cell division; and
5. All cells are basically the same in chemical composition and metabolic activities.
The Structure of the Cell

Both prokaryotic and eukaryotic cells

possess a plasma membrane and a
cytoplasm. The plasma membrane is the
outermost surface of the cell and it
separates the cell from its environment.
The cytoplasm is the aqueous content of
the cell, in which the cell's organelles
are suspended.

The plasma membrane is a semi-permeable

membrane that is present in all cells. The plasma
membrane is composed of carbohydrates, proteins,
phospholipids, and cholesterol. The plasma
membrane contains a lipid bilayer, which is termed
as such because it contains two layers of fat cells
organized into two sheets. It is typically about five
nanometers thick and surrounds all cells, providing
the membrane structure. The structure of the lipid
bilayer explains its function as a barrier. Lipids are
fats, such as oils, that are insoluble in water. There
are two important regions of a lipid that are crucial
for the lipid bilayer. Each lipid molecule contains a
hydrophilic region (the polar head region) and a
hydrophobic region (the nonpolar tail region). The
hydrophilic region is attracted to water conditions while the hydrophobic region is repelled from these
conditions. Since lipid molecules contain both regions, they are termed as amphipathic molecules. The
most abundant types of lipids found in the plasma membrane are phospholipids. It has two nonpolar
fatty acid chain groups and a tail. The tail is composed of a string of carbons and hydrogens. Due to its
double-bond structure, the tail has a kink. The bilayer is where the lipids organize themselves to hide
their hydrophobic region and to expose their hydrophilic regions. The organization as such is a
spontaneous process, which does not require energy. The most important property of the lipid bilayer is
that it is a highly impermeable structure. This means that molecules cannot freely pass across the lipid
bilayer. Only water and gas can pass through. It also means that large molecules and small polar
molecules cannot cross the bilayer, and thus, the cell membrane, without being assisted by other
structures. Another important characteristic of the lipid bilayer is its fluidity. The fluidity of the bilayer
allows proteins to move within it. The fluidity of the bilayer is also important because it allows
membrane transport. Fluidity is dependent on the temperature as well as the specific structure of the
fatty acid chains. Due to these two properties, the lipid bilayer was summarized by Singer and
Nicholson (1974) as the Fluid Mosaic Model. On the other hand, cells also contain a cytoplasm, which
is where organelles are suspended. The cytoplasm contains living components, which are cell
organelles, and nonliving components, which are ergastic substances and cytoskeletal elements. Without
the organelles, the cytoplasm is termed as cytosol. It is a jelly-like, semi-fluid matrix that is found
between the nuclear membrane and the cell membrane. The cytoplasm often comprises up to 50% of
the cell's volume. Aside from providing structural support for the cell, the cytoplasm is also where
protein synthesis occurs.

The cytoskeletons are another cell component that gives the cell its structure. It also allows the cell to
adapt. Thus, cells can reorganize their cytoskeletal components in order to change their shapes. The
cytoskeleton also has 'tracks' where it allows organelles to move around the cell. The cytoskeleton can
also move entire cells in multicellular organisms. Therefore, the cytoskeleton is involved in intercellular
communication. The cytoskeleton is composed of three different types of protein filaments: intermediate
filaments, microtubules, and actin. Briefly, actin is the main component of actin filaments. They are
double-stranded, thin, and flexible structures. It is also the most abundant protein in eukaryotic cells.
Microtubules are long, cylindrical structures composed of tubulin. They are organized around a
centrosome. These filaments provide tracks upon which organelles can move inside the cells.
Intermediate filaments are rope-like and fibrous. They have a diameter of approximately 10
nanometers. These filaments, however, are not found in all animal cells, but only in those where they
function to form the nuclear lamina.

The nucleus of the cell is one of the largest organelles found in cells. It also plays an important
biological role. It comprises close to 10% of the cell's volume and it is found near the center of
eukaryotic cells. The importance of the nucleus lies in its function as the storage space for DNA. The
cell nucleus is composed of two layers which form an envelope around the cell and only allows selected
molecules to enter and leave the cell. The DNA that is found in cells is packaged in chromosomes. The
nucleus directly comes into contact with the endoplasmic reticulum. It is also the site of DNA and RNA
synthesis. The mitochondria, on the other hand, is a double-membrane structure that is highly
specialized. It generates adenosine triphosphate (ATP), which provides organisms with energy. The
outer membrane of the mitochondria is smooth, while the inner membrane produces finger-like
infoldings called cristae. The inside of the mitochondria is filled with the homogenous, granular
mitochondrial matrix. This matrix has mitochondrial DNA, RNA, lipids, proteins, enzymes, and 70s
ribosomes. The endoplasmic reticulum is a network of tubular structures found in the cytoplasm and is
bound by a membrane. It extends from the nuclear membrane to the cell membrane. The endoplasmic
reticulum exists as oval vesicles, unbranched tubules, and flattened sacs called cisternae. There are two
types of endoplasmic reticulum: smooth and rough. The former does not contain ribosomes, while the
latter contains 80s ribosomes. The function of the endoplasmic reticulum is that it helps in intracellular
transportation. It also provides mechanical support for the cytoplasmic matrix, and it helps in the
formation of the Golgi complex and nuclear membrane. It is also the storehouse of lipids,
carbohydrates, and metabolic wastes.

Golgi bodies (Golgi complex) are a group of curved, flattened, plate-like cisternae. The cisternae
produce a network of tubules from the periphery. These tubules also end in vesicles. The Golgi
complex is also known as the packaging center of the cell. These bodies package proteins,
carbohydrates, etc. in their vesicles. They also produce enzymes called lysosomes, which are "suicide
bags" of the cell and result in cell death. They secrete enzymes, hormones, and material from the cell
wall. Plastids are found in plant cells and euglenoids. They are classified based on the type of pigment
that they contain. Chromoplasts contain carotenoids. Leucoplasts store food materials and are
colorless (is a type of plastid). Chloroplasts are green in color and function in photosynthesis.

Vacuoles are single-membrane bound sacs that are present in the cytoplasm. Plant cells have large
vacuoles and animal cells have small vacuoles. The tonoplast is the term for the membrane of the
vacuoles. It is filled with cell sap, which is watery. The cell sap has sugars, salts, pigments, and
enzymes. There are four types of vacuoles: contractile vacuoles, food vacuoles, gas vacuoles, and
storage vacuoles. Ribosomes produce proteins in cells. These are granular, non membranous structures
inside the cells. They are present in the cytoplasm, mitochondria, and chloroplast. Eukaryotes have 80s
ribosomes in the cytoplasm and 70s ribosomes in the plastids and mitochondria. Centrosomes form
spindles during cell division. They are surrounded by a denser type of cytosol called the centrosphere.
Centrosomes have two cylindrical structures called centrioles at the center.

Photosynthesis - Photosynthesis is the process by which plants that contain chlorophyll convert energy
from the sun into photochemical energy. This energy is stored in the form of carbohydrates.
Carbohydrates provide food for man and other heterotrophic organisms. Aside from this,
photosynthesis also produces oxygen as a by-product that is essential for all life on earth. The
photosynthetic activity from previous eras in geology have provided us with large deposits of fuel.
Lately, however, the by-products produced through photosynthesis are undergoing scrutiny, in part
because it is in danger of being inadequate for animal and human survival. Thus, understanding the
process of photosynthesis will help us gain an understanding of how its efficiency can be improved, and
in devising artificial sources of photochemical energy based on it. In addition to this, many biochemical
processes, such as electron transport, can be understood through photosynthesis. In the photosynthetic
activity of green plants, CO2, H2O, and light energy react with each other, producing 02 and
carbohydrates (CH20) as its products
.
Molecules of pigment, especially chlorophyll, various enzymes, and electron carriers act in a manner
that is catalytic in this reaction. The overall bioenergetics of this reaction can be summarized as
follows: C, H, and In COz and H2O are converted from a very stable arrangement of atoms to a less
stable arrangement of the same electrons and nuclei (CH20 + 02). In order for this process to occur,
light energy is needed. The total energy stored is 112 kcal/mole difference. The difference is supplied
by the energy from light. Photosynthesis is considered as an oxidation-reduction reaction. In addition to
green plants, certain kinds of bacteria (eg. purple and green) are capable of photosynthesis.
Photosynthetic bacteria are different from plants in that they are not capable of oxidizing H20.
Consequently, no oxygen is involved in the photosynthesis of bacteria. (two main types in plants are
chlorophyll a and chlorophyll b.)

Primary Events in Photosynthesis

Light absorption is the first step in

photosynthesis. There are three main
groups of pigments involved in light
absorption: chlorophylls, phycobilins, and
carotenoids. These pigments function as a
means for plants to absorb light through
the visible spectrum. The energy is then
transferred to reaction centers, where it is
used for photochemical reactions. The bulk
of the pigments involved in absorbing light
are called light-harvesting pigments.
There are two kinds of chlorophyll in
plants and green algae: chlorophyll A (Chl
a) and chlorophyll b (Chi b). These
pigments are soluble in organic solvents.
On the other hand, carotenoids are yellow
and orange pigments that are found in
almost all photosynthetic organisms. They
are also soluble in organic solvents. There
are two kinds of carotenoids: carotenes, of which beta-carotene is the most common, and carotenoids,
or alcohols. Phycobilins are water-soluble pigments, which are present in blue and red algae. They are
open-chain tetraphyroles. There are also two kinds of phycobilins: phycocyanins, which are primarily
found in blue-green algae, and phycoerythrins, which are found in red algae. Light emission is the
second step in photosynthesis. The Chl a molecule becomes excited due to direct light absorption.
These molecules undergo fluorescence (third step). After fluorescence, delayed light emission occurs.
Photosynthetic organisms emit light for short periods of time.

The third step is energy transfer and migration. Through a maze of several hundred Chl a molecules,
energy migration occurs until the energy reaches the reaction center where it can be converted into
chemical energy. There are two processes in energy transfer and migration: heterogenous, when the
energy is transferred to other Chl a molecules, and homogenous, when energy is transferred through
the same kinds of molecules.

The fourth step is the reaction at reaction centers. This is the process by which energy reaches reaction
centers and is converted into chemical energy. This reaction produces an oxidizing and reducing
equivalent. The primary electron in this process is reduced and the reaction center undergoes oxidation.
In tum, this receives an electron from the primary electron donor. This transfer of electrons is
summarized in the Calvin cycle. After electrons are transferred, the products of oxygen and
carbohydrates are created.

- Cisternae: comprise the Golgi bodies/complexes

- Chl a: chlorophyll A

Week 8: Perpetuation of Life

Plant Reproduction - The reproduction of plants is important for the propagation of life on
earth. Plants reproduce through three types: asexual, sexual, and vegetative.

Asexual Reproduction - In the asexual mode of reproduction, offspring are produced from the
vegetative unit produced by a parent without any fusion of sex cells or gametes. In addition to this, only
a single parent is involved and the offspring produced are genetically identical to the parent. There are
also several types of asexual reproduction. Fission can be seen in unicellular organisms such as yeast or
bacteria. The content of the parent cell divides into 2, 4, or 8 daughter cells. Accordingly, fission may
be called binary (2) or multiple (4 or more). Each daughter cell that is newly formed grows into a new
organism. Budding is bud-like growth formed on one side of the parent cell. As soon as the bud
separates from the parent cell, it becomes a whole new organism (e.g. yeast).

Fragmentation occurs in filamentous algae. It occurs as a result of accidentally breaking off a filament
into many fragments. Each new fragment may give rise to a new organism through cell division (e.g.
Spirogyra). Spore formation occurs in lower plants, such as pteridophytes and bryophytes. During this
type of asexual reproduction, special reproductive units develop asexually on the body of the parent.
These special reproductive units are called spores. These are microscopic units and are covered by
protective walls. Once spores reach an environment that is conducive to growth, they develop into new
plant bodies (eg. bread molds, mosses, fems).

Vegetative Reproduction - Vegetative reproduction involves the formation of new plants from a
somatic, or vegetative cell, or buds or organs of the plant. Here, a vegetative part of the plant, such as
the root, stem, leaf, or bud, is detached from the body of the parent and grows into a daughter plant
that is independent. It is similar to asexual reproduction in that it only requires mitotic division. Thus,
no gametic fusion occurs and daughter plants are exact genetic copies of their parents.

Sexual Reproduction - Sexual reproduction involves the fusion of female and male reproductive cells
(gametes). These gametes are haploid, which means that they contain only half the genetic material
(chromosomes) for a new organism to exist. The fusion of gametes is also called fertilization and it
results in the production of diploid zygote. When the zygote undergoes further development, it gives
rise to a new individual that is diploid. At the beginning stages of sexual reproduction, meiosis occurs.
The offspring are genetically different to their parents.

Reproduction in Lower Plants - Two representative plants that are considered lower plants are
Spirogyra (multicellular) and Chlamydomonas (unicellular). The unicellular algae, Chlamydomonas, is
a haploid, unicellular algae that is found in freshwater ponds. The plant's body is pear-shaped, and
There are two flagella attached to the narrow end. Flagella are filaments found in flagellates. A large
chloroplast is present. Towards the center of the organism, a nucleus is present. The chloroplast of
Chlamydomonas contains a single pyrenoid. The organism may undergo sexual or asexual
reproduction. When it undergoes asexual reproduction, it is through zoospores. Consequently, its
flagella is lost and the organism becomes non-motile. The protoplasm divides mitotically and forms 4-8
zoospores. Each zoospore develops a cell wall and it also grows into an adult cell. The parent cell,
however, does not exist anymore. During sexual reproduction of the Chlamydomonas, the cell again
becomes non-motile by losing its flagella. The protoplasm also divides mitotically into 2,4,8,16, and
132 daughter cells. Each daughter cell then develops its own flagella and is released to the water by the
rupture of the mother cell wall. Each daughter cell acts as a gamete. The gamete is morphologically
identical (isogamous). Two gametes released from the mother cell fuse together.

The contents of the gametes then fuse and form a zygote (diploid). This is the only stage in
the organism's life cycle that is diploid. The zygotes then develop a thick wall around itself
(zygospores). Then, the zoospore grows into a new organism. On the other hand, Spirogyra is a free-
floating algae found in freshwater ponds. The body contains a row of rectangular cells that are joined
end to end (filamentous alga). Each cell has a spiral ribbon-shaped chloroplast that contains many
pyrenoids. (Spirogyra are not considered angiosperms)

The nucleus is present in the cental vacuole with support from cytoplasmic strands. It undergoes two
types of reproduction: vegetative reproduction by fragmentation and sexual reproduction. Vegetative
reproduction by fragmentation occurs first when filaments break into smaller fragments. Then, each
fragment grows into a new organism by cell division. On the other hand, sexual reproduction occurs in
the organism. Scalariform conjugation, which is when filaments conjugate to form a ladder-like
appearance, starts when two filaments lie very close to each other. The cells of the two filaments
connect with each other through a conjugation tube. The contents of the cytoplasm of each cell rounds
off to act as a separate gameter. The gamete from one cell (male) passes into the conjugation tube
towards the other cell (female). The contents of these two gametes fuse to form a diploid zygote.

Reproduction in Angiosperms (Flowering Plants) - Angiosperms may reproduce vegetatively or

sexually. Sexual reproduction occurs by the fusion of male and female gametes that are present in the
flower. Thus, the plant's basic reproductive unit is the flower. Angiosperms can be classified according
to the following:

● Annuals: these plants live for only one year. The plants that produce seeds and flowers within
just one season are termed as annuals (e.g. peas).

● Biennials: plants that live for two seasons, and complete their life cycles within these two
seasons. During the first year, the plant is in a vegetative state. In the second year, the plants
produce flowers, fruits, or seeds and then they perish (e.g. radish).

● Perennials: plants that live for several years. The vegetative state of these plants may last from
one year to several years. In the year following their vegetative state, they produce flowers,
seeds, or fruits (eg. mangoes).

● Monocarpic: perennial plants that reproduce only once during their lifetime and then die (e.g.
bamboo).
Initiation of Flowering - When the plant's seed germinates, plantlets emerge from it. The young plant
grows and continues to grow until it has a definites shape and size. The plant's vegetative parts (root,
stem, leaves) must be well-developed. This phase in the plant's life cycle is known as the young of
juvenile phase. After the plant completes vegetative growth, the plant then enters into the reproductive
phase, or the adult phase. A vegetative shoot apex then transforms into a floral apex, a reproductive
part, and starts bearing flowers. The flowering stage may last from several days to several years. A
juvenile shoot has a soft stem, and only bears a few leaves. The size and shape of the leaves remain the
same. It does not respond to stimuli nor does it produce flowers. On the other hand, an adult shoot has
well-developed stems and leaves. The size and shape of the leaves change. It also responds to stimuli
and can produce flowers. Factors Affecting Flowering The plant's flowering is affected by light
(photoperiodism) and by temperature (vernalisation).

Vemasilation is when low temperatures occur, and this stimulates the early formation of flowers. On
the other hand, photoperiodism is the response of the plant to the duration of dark and light per day.
This determines its growth and flowering. The sex of a flower may be bisexual, which means that they
have both carpels and stamens, or unisexual (having only a staminate or pistillate). The sexual
determination of flowers may vary in dioecious species. However, sex determination may have a
chromosomal basis. The plants may also exhibit different levels of substances required for growth. For
instance, Cucumis, which bear male flowers, have high levels of gibberellin as compared to those that
bear only female flowers. Gibberellin is a plant hormone that assists in growth and reproduction.
(Ghibberellin may induce the formation of functional female flowers on male plants) When gibberellin
is applied externally, the production of male flowers may be induced even in plants that are genetically
female. Conversely, treating male plants with ethylene or auxin may induce the development of
functional female flowers. The latter response has been seen in Cannabis.

Parts of a Flower

A typical flower consists of four whorls which are located on a stalk (thalamus). Sepals
comprise the calyx. Petals comprise the corolla. Additionally, stames comprise the androecium
and pistils (gynoecium) consists of carpels. The two outer whorls are known as non-essential or
accessory whorls because they do not play a part in the plant's reproduction, although they aid
indirectly. The two inner whorls, the androecium (male plant reproductive organ) and the
gynoecium (female reproductive organ) are termed as essential whorls because they are the
main components of the plant's reproduction.

Stamen, Microsporangia, and Pollen Grain - The plant's stamen consists of an anther that contains
microsporangia, or four pollen sacs. These are supported by a slender filament. Each sporangium
contains masses of large cells. These cells show a prominent nucleus and abundant cytoplasm. These
cells are also known as the sporangeous or the microspore mother cells. Each microsporangium is made
up of distinct layers of cells when mature. The outermost layer is the epidermis. It has a middle
layer of cells with thin walls. The innermost layer is the tapetum, which consists of large cells. The
tapetum nourishes the developing grains of pollen cells. Microspore mother cells undergo meiosis. Each
mother cell produces four haploid microspores (diploid pollen grains) that are arranged in a tetrad

The Development of the Male Gametophyte - The wall of the microspore consists of two principal
layers. The outer layer is the exine and thin spaces (germ pores). The exine layer is made up of a
durable substance called sporopollenin. The pollen tube grows out of the pollen grain through the germ
pores. The inner layer is the cellulosic wall (the intine). The microspore moves towards the periphery.
The cell then divides into a small generative cell and a large vegetative cell. At this stage, the pollen are
released by the rupture of the stodium dehiscence of the anther. The pollen grain itself is not a male
gamete. Rather, it produces the male gamete and is therefore a male gametophyte.

The Development of the Female Gametophyte - The main part of the ovule is bounded by two
coverings (integuments). These integuments leave behind a small aperture, or opening. The ovule is
attached to the ovary via a stalk, known as the funiculus. The basal part of this structure is the chalaza.
The female gamete's gynoecium (pistil) represents its reproductive part. Each pistil is composed of a
stigma, ovary, and style. The ovary contains one or more ovules (megasporangia), which act as future
seeds. An ovule develops as a type of projection from the placenta in the ovary. It consists of
integuments and nuclei. As the ovule grows, it becomes raised on the stalk, termed as funiculus.This is
attached to the placenta on the other end.

Within the nucleus, a single hypodermal cell becomes larger and it becomes the megaspore mother cell.
This cell undergoes meiotic division, and then gives rise to four haploid megaspore cells. Usually, three
of the megaspores degenerate, while one remains as the functional megaspore. Thus, 8 nuclei are
formed as a result of this division. The enlarged structure, shaped like an oval and with 8 nuclei, is
known as the embryo sac. The nuclei then migrate and form three groups. Cell membranes and nuclei
develop around the nucleus, except the two at the center of the sac, which is now termed as the central
cell.

Vegetative Reproduction in Angiosperms - The natural method of the vegetative reproduction of

angiosperms starts with the underground modification of stems, such as ginger, potato, onion, and
corn. These are provided with buds which develop into a new plant and are therefore used to carry out
vegetative propagation of the plant in the filed. Plants with subaerial modification, such as
chrysanthemum and pistia, are also used for vegetative propagation. Artificial methods of vegetative
reproduction includes the use of cuttings, layering, and aerial layering.

Animal Reproduction - Animal reproduction is the process by which animals propagate on

earth and it is also the process through which genetic materials are transferred to offspring. Animals,
like plants, may reproduce through asexual or sexual means. Asexual reproduction is primarily
employed by tunicates, protists, and cnidaria. However, it may also occur in the more complex animal
species. Indeed, the formation of identical twins by the separation of two identical cells in the early
embryo is a form of asexual reproduction. Through mitosis, genetically identical cells are produced
from one parent cell. This permits asexual reproduction to occur in protists by the organism 's division,
called fission.

Cnidaria commonly reproduce by budding, which is when a part of the parent's body is separated from
the rest and differentiates into a new organism. The new organism may become independent, or it may
remain attached to the parent organism, forming a colony. Sexual reproduction occurs when a new
individual is formed from the union of two sex cells, or gametes. Gametes include the sperm and the
egg. The union of these two produces a fertilized egg, or zygote. Through mitotic division, the zygote
develops into a new organism. The zygote and the cells that it forms are diploid. This means that they
contain both members of each pair of homologous chromosomes. The gametes are formed in the sex
organs, or gonads (the testes and the ovaries), and are haploid. The process of sperm formation
(spermatogenesis) and egg formation (oogenesis) are also included in the study of the reproduction of
animals.

Different Approaches to Sex - Virgin birth, or parthenogenesis, is common in many species of

arthropods. Some species are exclusively parthenogenetic (all female), while others switch between
generations. Another variation in the reproductive strategies used by animals is hermaphroditism. This
is the case when one individual has both testes and ovaries. Tapeworms are hermaphroditic, and it is
able to fertilize itself.

However, most hermaphroditic animals require another organism to reproduce, such as in the case of
two earthworms. There are also some deep sea fish which are hermaphrodites, meaning that they are
both male and female at the same time. Numerous species of fish can change their sex, a process
which is called sequential hermaphroditism. The change from female to male is protogyny, while the
change from male to female is protandry.

Sex Determination - In fish, there are conditions which cause changes in sex. In mammals, however,
sex is already determined early in embryonic development. The reproductive systems of both males and
females (humans) are identical during the first 40 days of embryonic development. During
this time, the cells that will give rise to either ova or sperm move from the yolk sac to the embryonic
gonads. These gonads can become testes in males and ovaries in females. For this reason, embryonic
gonads are said to be different.

If the embryo is a male, it will posses a Y chromosome. If the embryo is a female, it will have no Y
chromosomes. Recent evidence suggests that the sex-determining gene (SRY) appears to have been
highly conserved during the evolution of vertebrate groups. Once the testes are formed in the embryo,
they secrete testosterone and other hormones that will promote the development of the external genitalia
of the male, as well as accessory reproductive organs. In other words, all embryos are females until
they are masculinized by testosterone.

Fertilization and Development - There are two types of fertilization: internal and external. Extemal
fertilization commonly occurs among organisms in the ocean, where water allows for the rapid
dispersion of sperm or ova towards others of the same species. On the other hand, internal fertilization
is common in terrestrial animals. Internal fertilization is the introduction of the male gamete into the
female's reproductive tract. Vertebrates that practice internal fertilization have three strategies:

● Oviparity, which is found in some amphibians, fish, and some reptiles, is when the eggs are
deposited outside the mother's body after fertilization.
 ● Ovoviviparity is commonly found in mollies, guppies, and mosquito fish. The fertilized eggs are
retained within the mother in order to complete their development. The embryos still take all of
their nourishment from the egg yolk. The young are thus fully developed when they hatch.
● Viviparity is found in almost all mammals. The young develop within the mother and take its
nourishment directly from their mother's blood, as opposed to egg yolks.

Reproduction in Fish and Amphibians - In most species of bony fish (teleosts), the fertilization of
eggs occurs externally. The eggs contain only enough yolk to sustain the developing embryo until it is
ready to teach. The development of fish is rapid, and the young are able to find their own food source
from a very young age. Although thousands of eggs are fertilized during a mating period, most of the
eggs perish. In most cartilaginous fish, however, most fertilization is internal. The male introduces
sperm into the female by means of a modified pelvic fin. In these vertebrates, the development of the
young is viviparous.

Amphibians use external fertilization in most cases. In these organisms, gametes from the males and
females are released through the cloaca. Most amphibian eggs develop in the water. The time required
for amphibians to develop is much longer than fish. However, amphibian eggs do not have a lot of
yolk. Instead, the process of amphibian development is divided into embryonic, larval, and adult stages.

Reproduction in Reptiles and Birds - Most reptiles and birds are oviparous. That is, after their eggs
have been fertilized, they are deposited outside of the mother's body in order to complete their
development. As with most animals that fertilize internally, male reptiles have a penis that they use to
introduce male gametes into the female's reproductive tract. The shells of reptile eggs are leathery, and
this allows for better withstanding of environmental conditions. All birds practice internal fertilization,
although most birds lack a penis. In some of the larger birds (e.g. ostriches, geese, and swans), the
male cloaca can extend to form a false penis. As the eggs passes through the oviduct, the glands secrete
the egg whites and the hard shells that distinguish bird eggs from reptilian eggs.

Most birds are also homeotherms, meaning that they keep a stable body temperature. Thus, they often
incubate their eggs after laying them to keep them war. The young that emerge from bird eggs do not
develop rapidly, and they need to be assisted and fed by their parents until they are ready to be
independent. Bird and reptile eggs show the stark evidence for adaptation to land. These eggs are
termed as amniotic eggs because the embryo that develops within the cavity filled with fluid is
surrounded by a membrane called an amnion. The amnion is an extra-embryonic membrane and
develop outside of the body of the embryo. Other extra-embryonic membranes include the chorion, the
yolk sac, and the allantois.

Reproduction in Mammals - The reproductive cycles of mammals differ greatly. Some are
seasonal breeders that reproduce only once a year. Others have shorter reproductive cycles. Among
those that have short reproductive cycles, females usually undergo the reproductive cycle, while males
are more constant in their reproductive activity. Ovulation in females is the cyclic release of an egg
from the ovary. Most mammals are fertile only at the time of ovulation. The period of sexual
receptivity is called estrus, and the reproductive cycle is therefore called an estrous cycle.

The estrous cycle of most mammals changes according to the secretion of follicle-stimulating hormone
(FSH) and luteinizing hormone (LH). These are secreted by the anterior pituitary gland and cause
changes in egg cell development and hormone secretion in the ovaries. Like other mammals, humans
and apes have an estrous cycle. However, unlike other mammals, humans and apes can mate anytime
during their reproductive cycle. The most primitive mammals, the monotremes, are oviparous.

The marsupials (e.g. kangaroos) give birth to offspring that are already completely developed. The
placental mammals retain their young for a much longer period within the mother's uterus. The fetuses
are nourished by the placenta, which is derived from the chorion and the uterine lining of the mother.
The fetus derives its nutrients from the mother's blood, since fetal and maternal blood vessels are in
close proximity

Overview of Genetics

The most fundamental characteristic of all living

things is the ability to reproduce. All organisms
gain their genetic material from their parents.
Genetic information determines their structures
and functions by directly influencing the synthesis
of proteins. Genes and Chromosomes Gregor
Mendel deduced the classical principles of genetics
in 1865. He based his deductions on the results of
breeding experiments with peas. Characteristics of
the peas, such as seed color, could be predicted by
Mendel through the determination of a pair of
inherited factors. These inherited factors are now
called genes. One gene copy, which is termed as
an allele, specifies a certain trait that is inherited from each parent. A gene is said to be dominant if it
contains alleles for two colors, and only one color shows.

For instance, breeding yellow and green peas yields yellow peas. In this case, the yellow is said to be
the dominant gene while green is said to be recessive. If Y designates yellow and y designates green,
then the genetic composition (genotype) of the peas is Yy, and their physical appearance (phenotype)
is yellow. Mendelian genetics is the term for the deductions of Mendel. Shortly after, the role of
chromosomes as carriers of genes was proposed. It was also realized that higher animals and plants
have diploid cells, which contain two copies of each chromosome. Cell division in the form of meiosis
involves the daughter cell inheriting only one member of each chromosome pair. Consequently, the
sperm and egg are haploid cells (diploid cells) at fertilization, and this creates diploid organisms.
Experiments on the fruit fly, Drosophila melanogaster, established most of the principles of genetics
today. The fundamentals of genetic linkage, mutation, and the relationships between chromosomes and
genes were elucidated. Genetic alterations were observed in Drosophila in the 1900s. These involved
readily observable traits, such as eye color and wing shape. This experiment showed that there are traits
which are inherited in pairs, which are said to be linked genes. Chromosomes exchange materials
during meiosis, leading to the linked genes' recombination. The frequency of recombination between
two linked genes depends on their distance from each other on the chromosome. Thus, the frequency
with which different genes recombine can be used for mapping their positions on chromosomes,
which is known as genetic mapping.

Genes and enzymes

The first evidence for the existence of enzymes came in

1909, through the study of the disease called
phenylketonuria. The disease results from a genetic defect
that results in problems with the metabolism of
phenylalanine, an amino acid. This defect was
hypothesized to result from a lack of enzymes needed to
catalyze the metabolic reaction. Subsequently, this led to
the suggestion that genes also specify the synthesis of
enzymes. Understanding the chromosomal basis of
heredity and the relationship between enzymes and genes
did not itself provide a molecular explanation for the
gene. Chromosomes, aside from containing DNA, also
contain proteins.

The structure of DNA is three-dimensional. We owe our

understanding of this structure to James Watson and
Francis Crick, who formed the basis for present-day
molecular biology. DNA is a polymer composed of four
nucleic acid bases: adenine (A), guanine (G), cytosine
(C), and thymine (T). The former two are purines, while
the latter two are pyrimidines. These bases are linked to
phosphorylated sugars. The central model of the DNA is
that it is double-helix with a sugar- phosphate backbone
on the outside of the molecule. On the inside, bases are
held together by hydrogen bonds that are formed between
purines and pyrimidines on opposite chains. The amount
of adenine is always equal to the amount of thymine, and
the amount of guanine to that of cytosine. Due to this
specific base pairing, two strands of DNA are
complementary: each strand contains the bases that are
required to specify the sequence of the other strand
Replication of DNA - The discovery of complementary base pairing between DNA strands suggest that
there is a molecular solution to the problem of how genetic material directs its own replication. Two
strands of DNA can separate to serve as templates for a new strand. This would be specified by base
pairing. This process is called semiconservative replication, because one strand is conserved in the
progeny DNA molecule. The enzyme that catalyzes DNA replication is DNA polymerase. The
replication of DNA can either be bidirectional, going both forwards and backwards, or unidirectional,
going only one direction. DNA polymerase adds nucleotides to the DNA chain in a specific direction,
which is from 5' to 3'.

DNA Transcription and Translation - Protein synthesis is directed by genes. When genes are
defective, they produce defective proteins and this results in abnormalities such as albinism. There are
two basic steps to the synthesis of protein. The first is the transcription of genes, which produces a
messenger RNA (mRNA) molecule. The second step to protein synthesis is translation. This is the
portion of protein synthesis in which the mRNA molecule is translated into proteins. During
transcription, the sequence of nucleotides in a gene in the DNA is copied to the corresponding sequence
of nucleotides in mRNA. During translation, the sequence of nucleotides in the mRNA determines the
sequence of amino acids in proteins.

DNA transcription is mediated by RNA polymerase. It separates the two strands of the double helix and
constructs an mRNA molecule by adding nucleotides one at a time. The base-pairing rule summarizes
which nucleotides pair with each other. Guanine pairs with cytosine, while adenine pairs with thymine.
DNA translation determines the sequence of amino acids in the protein. The cell uses transfer RNA
(tRNA) to bring the correct amino acid for each codon in the mRNA. Each tRNA has three
nucleotides that form an anticodon. The three nucleotides in the anti- codon are complementary to the
three nucleotides (three per codon) in the mRNA codon for a specific amino acid. Amino acids are the
building blocks of
proteins.