Transcript Welcome to Biology 122 - Home Page for Ross Koning

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The Organism as a Unit of Life
Cellular Structure (cell = unit of life)…one or many!
Metabolism = Homeostasis (PSN, Resp, N2fix, ferment, etc.)
Growth = irreversible change in size
Movement…includes internal, limbs, locomotion
Reproduction…failure = extinction
Acclimatization-short term responses = behavior
Adaptation-long term responses = evolution
Biology is multidimensional
Ecosystem
Community
Population
Organism
Organ System
Organ
Tissue
Cell
This array is an example of what
dimension?
Levels of Organization
What fields of biology are at each
extreme?
Biophysics and Biochemistry
In this course our focus will be upon…
The Organism!
This level of organization is also…
Hierarchial / Multidimensional!
Carolus Linnaeus (aka Carl von Linné)
Swedish Botanist,
Physician, and Zoologist
1707 - 1778
Developed a hierarchial
classification scheme
that we use to this day!
http://upload.wikimedia.org/wikipedia/commons/6/68/Carl_von_Linné.jpg
Taxonomy is also Hierarchial!
The Organisms are Diverse: Taxonomy
Domain
Bacteria
Archaea
Eukarya
Eukarya
Eukarya
Eukarya
Eubacteria
Gram +
Archaea
Protista
(Chromista)
Plantae
Fungi
Animalia
Phylum
Proteobacteria
Euryarchaeota
Phaeophyta
Anthophyta
Magnoliophyta
Basidiomycota
Chordata
Class
Gammaproteobacteria
--
Phaeophyceae
Dicotyledonae
Hymenomycetes
Mammalia
Order
Enterobacteriales
Halobacteriales
Fucales
Rosales
Agaricales
Primates
Family
Enterobacteriaceae
Halobacteriaceae
Fucaceae
Rosaceae
Agaricaceae
Hominidae
Genus
Escherichia
Halobacterium
Fucus
Rosa
Agaricus
Homo
Species
E. coli
H. salinarum
F. distichus
R. multiflora
A. bisporus
H. sapiens
Common
DH5
Halophytic
archaeon
Rockweed
Wild Rose
Mushroom
Human
Kingdom
Figure 1-5 Page
7 of 3rd edition of
your book
(deleted from
current edition)
KINGDOM
Not plants, fungi, etc.
(Animalia)
PHYLUM Not invertebrates
(Chordata)
CLASS
Not birds, reptiles, etc.
(Mammalia)
ORDER
(Primates)
Not bison, etc.
FAMILY
Not lemurs, monkeys etc.
(Hominidae)
GENUS
(Homo)
SPECIES
(Homo
sapiens)
Not chimps, gorillas, etc.
Not H. neanderthalensis, H.
floresiensis, etc.
Homo sapiens
Learn your own Latin binomial.
Our genus means “self” not gender identity
Our epithet: we think that we think!
Our epithet always ends in ‘s’:
One Homo sapiens is the instructor.
There are many Homo sapiens in class.
Print in italics, underscore in manuscript.
I am a Homo sapiens.
√
How many organisms are there?
Good Question! Let’s exclude extinct species!
Many extant are unknown so we estimate!
Bacteria: 10,000
Archaea: 1,000
Protista: 20,000
(includes Stramenopila and Rhodophyta)
Plantae: 285,000
(mostly flowering)
Fungi: 110,000
Animalia: 1,400,000
(mostly arthropods)
How many organisms are there?
What is a species?
Animal species concept…
if offspring are fertile then same species…
does not apply to species of other
kingdoms:
Prokaryotes (no sex)
Allopolyploidy in plants
Horse: Equus caballus
Donkey: Equus asinus
X
http://www.fotosearch.com/comp/JNB/JNB002/00099924.jpg
http://www.explorecrete.com/albums/album19/donkey.jpg
Mule: Sterile Hybrid
http://www.muleranch.com/Clients/RedPeak-JerryHeitzlerMule.gif
Wolf
Canis lupus
German Shepherd Dog
Canis familiaris
X
X
http://www.dog.com/breed/docgrafx/germshep.jpg
Coydog
Wolfdog
Fertile
Hybrids!
http://www.city.west-lafayette.in.us/wlpd/coyredw.jpg
http://www.leerburg.com/Photos/wolfdog-05.jpg
http://www.ecores.uzhgorod.ua/Fotogalereya/fauna/Canis_lupus_01.JPG
http://museum.utep.edu/chih/theland/animals/mammals/clatrans.jpeg
Coyote
Canis latrans
What is a Species? The Case of Bread Wheat
AA (diploid wheat)
x
Triticum urartu
DD (diploid grass)
Aegilops tauschii
AADD
AD (sterile diploid) colchicine
similar to mule!
or spontaneous (fertile tetraploid)
BB (diploid grass)
Aegilops speltoides
BBAADD
colchicine
BAD (sterile triploid)
Fertile hexaploid
or spontaneous
Bread Wheat
Triticum aestivum
Bread Wheat Created 7500 BC with spontaneous doubling of DNA
Levy A. A. and M. Feldman. 2002. The impact of polyploidy on grass genome evolution. Plant Physiol. 130: 1587-1593.
How many kingdoms are there?
Good Question!
The relationships among known organisms
are not completely understood.
Are you a lumper or a splitter?
Newer information appears to back up the
taxonomic decisions of splitters!
Historical shifts from 2, to 3, to 4, to 5, to 6
and now to many more in just the last 40
years!
Lumpers
Shifting Kingdoms
Splitters
2
3
5
6
8
Bacteria
Bacteria
Bacteria
Bacteria
Bacteria
Archaea
Archaea
Archaea
Archaea
Archaea
Archezoans
Archezoans
Archezoans
Archezoans
Archezoans
Euglenoids
Euglenoids
Euglenoids
Euglenoids
Euglenoids
Chrysophytes
Chrysophytes
Chrysophytes
Chrysophytes
Chrysophytes
Green Algae
Green Algae
Green Algae
Green Algae
Green Algae
Brown Algae
Brown Algae
Brown Algae
Brown Algae
Brown Algae
Red algae
Red algae
Red algae
Red algae
Red algae
Slime Molds
Slime Molds
Slime Molds
Slime Molds
Slime Molds
True Fungi
True Fungi
True Fungi
True Fungi
True Fungi
Bryophytes
Bryophytes
Bryophytes
Bryophytes
Bryophytes
Tracheophytes
Tracheophytes
Tracheophytes
Tracheophytes
Tracheophytes
Protozoans
Protozoans
Protozoans
Protozoans
Protozoans
Myxozoans
Myxozoans
Myxozoans
Myxozoans
Myxozoans
Multicellular
Animals
Multicellular
Animals
Multicellular
Animals
Multicellular
Animals
Multicellular
Animals
Charles Darwin - British Naturalist
Formal Studies: Medicine and Theology
1809 - 1882
Descent with
Modification
http://www2.biologie.unihalle.de/zool/mol_ecol/Bilder/DarwinBild.jpg
1880 The Power of
Movement in Plants
1871 Descent of Man
1859 Origin of Species
http://upload.wikimedia.org/wikipedia/en/3/3e/Charles_Darwin_1854.jpg
Species evolved from generation to generation over time
1831-1836 HMS Beagle Voyage
http://www.omniscopic.com/blog/uploaded_images/darwin-791061.jpg
Darwin’s Tree of Life (1859) the only figure in:
On the Origin of Species
future time
present
many
more
many
more
The Roman
numerals
each
represent
1000
generations
past time
The letters A-L represent
hypothetical progenitor species
within a single genus
Notice the very large number of extinctions!
http://upload.wikimedia.org/wikipedia/commons/f/f4/Darwins_tree_of_life_1859.gif
Question 14 Page 15
before nucleus
true nucleus
Turn back to the tree of life shown in Figure 1.5. Note that Bacteria and
Archaea are prokaryotes, while Eukarya are eukaryotes. On the simplified
tree below, draw an arrow that points to the branch where the structure
called the nucleus originated. Explain your reasoning.
DOMAIN
DOMAIN
DOMAIN
BACTERIA
ARCHAEA
EUKARYA
Extant
How Many Kingdoms?
8
5
3
Extinct
First Eukaryote!
2
1
Original Cell
Extant
How Many Kingdoms?
8
5
3
Extinct
First Eukaryote!
2
1
Original Cell
Here is a phylogeny that covers some of the animals:
http://thehurricanes.deviantart.com/gallery/
http://thehurricanes.deviantart.com/art/Phylogeny-with-Spongebob-156909686
Figure 1-9 Page
10 of 3rd Edition
Plants, fungi, and
animals are small
branch tips on
the tree of life
This node represents the common
ancestor of archaea and eukaryotes
This node represents the common
ancestor of all organisms alive today
Page 7 Figure 1.5
DOMAIN BACTERIA
Mycoplasma
How is this graphic
from your book the
same, and how is it
different from the
other depictions of
the “Tree of Life”
you have seen so
far?
In which direction is
the axis of time
shown?
The long list of
organisms down the
right are?
Firmicutes
Cyanobacteria
Actinobacteria
Spirochaetes
Chlamydiae
Bacteriodetes
-Proteobacteria
-Proteobacteria
-Proteobacteria
This node
represents the
common ancestor
of all organisms
alive today
-Proteobacteria
-Proteobacteria
DOMAIN ARCHAEA
Thaumarchaeota
Crenarchaeota
Korarchaeota
This node
Euryarchaeota
represents the
common ancestor
of archaea and
DOMAIN EUKARYA
eukaryotes
Slime molds
Fungi
Animals
Choanoflagellates
Euglenids
Parabasilids
Diplomonads
Red algae
Green algae
Land plants
Foraminiferans
Ciliates
Dinoflagellates
Apicomplexans
Water molds
Diatoms
Brown algae
Fungi,
animals,
and plants
are small
branch tips
on the
tree of life
In spite of this
graphic image, and
the highlighted point
on the lower right,
your book, like most
others, is organized
as if there were only
two kingdoms
(Plantae and
Animalia), as if
nothing happened
since Linnaeus!
The three twigs
highlighted on the
tree are showing
which level of
modern Linnean
taxonomy?
David Hillis’
tree of life
based on total
genome
sequences (at
the time)
Eukaryotes
Archaeons
How many
twigs would be
on this diagram
if ALL the
extant
organisms
were shown?
http://upload.wikimedia.org/wikipedia/commons/1/11/Tree_of_life_SVG.svg
?
Prokaryotes
Time
Dimension?
David Hillis’
tree of life
based on rRNA
sequence
analysis (at
press time)
Because this
analysis is
easier/faster,
more species
can be
included!
http://www.zo.utexas.edu/faculty/antisense/tree.pdf
origin
Why did the five-kingdom system of classification
fall out of favor?
A. It was too complex—the original two-kingdom system
of Linnaeus was more useful.
B. Many organisms were difficult to classify because they
had characteristics of more than one kingdom.
C. There were too many prokaryotes to be included in a
single kingdom.
D. It did not reflect the actual evolutionary relationships
among organisms very well.
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings/Addison-Wesley
Summary Points for Taxonomic/Phylogenetic Classification
• Linnaean Classification is hierarchical: Kingdom, Phylum, Class,
Order, Family, Genus, Species
• Organisms have names: Common names are redundant and
multiple, Latin binomials are universal and almost unique
• Species of organisms have a recognized binomial: Genus name
and specific epithet
• There are more than a million species of organisms on our planet-most are arthropods
• Many species on Earth are unknown or virtually unstudied
• Organisms are grouped into a few kingdoms
• The number of kingdoms has increased over time on the planet,
and in biology over time too
• Phylogenic Cladistics relates organisms based on evolutionary
pathways rather than on taxa
• All organisms on this planet evolved from a single ancestor and so
are a clade
• Most of the recognized Kingdoms are close to natural groupings
based on shared ancestry
• Kingdom Protista needs further dissection to become a natural
grouping
For Figuring Biological Data This Week!
Bring your Biologist at Work Worksheet (completed?)
Bring your Figuring Biological Data Worksheet (read!)
Bring your Laptop with Excel installed…if you have one
Bring your Flash Drive if you do not have a laptop
Download the Course Data file from the course website:
• To your Laptop with Excel…OR
• To your Flash Drive