" The Big Picture!" by Mr C

VSB Science Blog
10
Jul

Gap notes for Chapter 2

Biology 11 Ms. Jamieson

Questions

1) Write the meanings of the following terms:

a) Adaptation

b) Evolution

c) Population

d) Fossil

e) Species

2) Why is evolution such an important scientific concept?

Name: _________________________ Date: __________ Block: _____

Chapter 2 – Adaptation and Change Read pages 60 – 67, and answer the following questions:

Examples to illustrate your answers

Information from text

an inherited trait or set of traits that improve the chancs of survival and reproduction of oranisms

the process by which populations of living things change over a series of generations

a group of individuals of the same species occupying a given area at a certain time

a group of organisms that look alike and that can interbreed under natural conditions to producce fertile offspring

3) How are fossils formed?

4) What is the geological time scale?

5) What is the Burgess Shale, and where is it?

6) How old are the fossils in the Burgess Shale, and what period in the Earth’s history do they belong to? (see Fig. 2.6 page 64)

7) Why is the Burgess Shale so important?

8) How is the Burgess Shale evidence of divergent evolution

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes and have No Comments
10
Jul

Phylogeny and Systemics Notes

Biology 11 Outline Notes

Classification of Organisms

Overview
Phylogeny and Systematics

  • Evolutionary biology is about both process and history.
    • °  The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species.
    • °  A major goal of evolutionary biology is to reconstruct the history of life on earth.
  • In this chapter, we will consider how scientists trace phylogeny, the evolutionary history of a group of organisms.
  • To reconstruct phylogeny, scientists use systematics, an analytical approach to understanding the diversity and relationships of living and extinct organisms.
    • °  Evidence used to reconstruct phylogenies can be obtained from the fossil record and from morphological and biochemical similarities between organisms.
    • °  In recent decades, systematists have gained a powerful new tool in molecular systematics, which uses comparisons of nucleotide sequences in DNA and RNA to help identify evolutionary relationships between individual genes or even entire genomes.
  • Scientists are working to construct a universal tree of life, which will be refined as the database of DNA and RNA sequences grows.

    A. Phylogenies Are Based on Common Ancestries

    1. Sedimentary rocks are the richest source of fossils.

  • Fossils are the preserved remnants or impressions left by organisms that lived in the past.
  • In essence, they are the historical documents of biology.
  • Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and swamps, where the minerals settle to the bottom along with the remains of organisms.
    • °  As deposits pile up, they compress older sediments below them into layers called strata.
    • °  The fossil record is the ordered array in which fossils appear within sedimentary rock strata.

       These rocks record the passing of geological time.

    • °  Fossils can be used to construct phylogenies only if we

      can determine their ages.

    • °  The fossil record is a substantial, but incomplete, chronicle of evolutionary change.

See Chapter 17

Notes

Review: Genetics
Read text chp 10 “DNA, RNA, and

Protein Synthesis.” This content is also required for Biology 12.

Conserved Sequences

are similar or identical sequences that may occur within nucleic acids (e.g., DNA), proteins or polymeric carbohydrates within multiple species of organism or within different molecules produced by the same organism. In the case of cross species conservation, this indicates that a particular sequence may have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is said to be.

Sequence similarities serve as evidence for structural and functional conservation, as well as of evolutionary relationships between the sequences.

Evolution: Taxonomy

8/5/07

Classification of Organisms

Notes

  • °  The majority of living things were not captured as fossils upon their death.

     Of those that formed fossils, later geological processes destroyed many.

     Only a fraction of existing fossils have been discovered.

  • °  The fossil record is biased in favor of species that existed for a long time, were abundant and widespread, and had hard shells or skeletons that fossilized readily.

    2. Morphological and molecular similarities may provide clues to phylogeny.

  • Similarities due to shared ancestry are called homologies.
  • Organisms that share similar morphologies or DNA sequences are likely to be more closely related than organisms without such similarities.
  • Morphological divergence between closely related species can be small or great.

° Morphological diversity may be controlled by relatively few genetic differences.

  • Similarity due to convergent evolution is called analogy.
    • °  When two organisms from different evolutionary lineages experience similar environmental pressures, natural selection may result in convergent evolution.

       Similar analogous adaptations may evolve in such organisms.

    • °  Analogies are not due to shared ancestry.
  • Distinguishing homology from analogy is critical in the

    reconstruction of phylogeny.

    • °  For example, both birds and bats have adaptations that allow them to fly.
    • °  However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb that to a bird’s wing.
    • °  Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors.
    • °  Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing.
  • Analogous structures that have evolved independently are also called homoplasies.
  • In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently.

° For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones.

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Classification of Organisms

Notes

  • °  The two skulls match almost perfectly, bone for bone.
  • °  It is highly unlikely that such complex structures have

    separate origins.

  • °  More likely, the genes involved in the development of both skulls were inherited from a common ancestor.
  • The same argument applies to comparing genes, which are sequences of nucleotides.
  • Systematists compare long stretches of DNA and even entire genomes to assess relationships between species.

° If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous.

  • It may be difficult to carry out molecular comparisons of nucleic acids.
    • °  The first step is to align nucleic acid sequences from the two species being studied.
    • °  In closely related species, sequences may differ at only one or a few sites.
    • °  Distantly related species may have many differences or sequences of different length.

       Over evolutionary time, insertions and deletions accumulate, altering the lengths of the gene sequences.

  • Deletions or insertions may shift the remaining sequences, making it difficult to recognize closely matching nucleotide sequences.

° To deal with this, systematists use computer programs to analyze comparable DNA sequences of differing lengths and align them appropriately.

• The fact that molecules have diverged between species does not tell us how long ago their common ancestor lived.

° Molecular divergences between lineages with reasonably complete fossil records can serve as a molecular yardstick to measure the appropriate time span of various degrees of divergence.

  • As with morphological characters, it is necessary to distinguish homology from analogy to determine the usefulness of molecular similarities for reconstruction of phylogenies.
    • °  Closely similar sequences are most likely homologies.
    • °  In distantly related organisms, identical bases in otherwise different sequences may simply be coincidental matches or molecular homoplasies.
  • Scientists have developed mathematical tools that can distinguish “distant” homologies from coincidental matches in extremely divergent sequences.

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Classification of Organisms

Notes

° For example, such molecular analysis has provided evidence that humans share a distant common ancestor with bacteria.

• Scientists have sequenced more than 20 billion bases worth of nucleic acid data from thousands of species.

B. Phylogenetic Systematics: Connecting Classification with Evolutionary History

  • In 1748, Carolus Linnaeus published Systema naturae, his classification of all plants and animals known at the time.
  • Taxonomy is an ordered division of organisms into categories based on similarities and differences.
  • Linneaus’s classification was not based on evolutionary relationships but simply on resemblances between organisms.

° Despite this, many features of his system remain useful in phylogenetic systematics.

1. Taxonomy employs a hierarchical system of classification.

  • The Linnaean system, first formally proposed by Linnaeus in Systema naturae in the 18th century, has two main characteristics.
    • Each species has a two-part name.
    • Species are organized hierarchically into broader and

      broader groups of organisms.

  • Under the binomial system, each species is assigned a two-

    part Latinized name, a binomial.

    • °  The first part, the genus, is the closest group to which a

      species belongs.

    • °  The second part, the specific epithet, refers to one

      species within each genus.

    • °  The first letter of the genus is capitalized and both names

      are italicized and Latinized.

    • °  For example, Linnaeus assigned to humans the optimistic scientific name Homo sapiens, which means “wise man.”
  • A hierarchical classification groups species into increasingly broad taxonomic categories.
  • Species that appear to be closely related are grouped into the same genus.

° For example, the leopard, Panthera pardus, belongs to a genus that includes the African lion (Panthera leo) and the tiger (Panthera tigris).

• Genera are grouped into progressively broader categories: family, order, class, phylum, kingdom, and domain.

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Classification of Organisms

Notes

• Each taxonomic level is more comprehensive than the previous one.

° As an example, all species of cats are mammals, but not all mammals are cats.

• The named taxonomic unit at any level is called a taxon.

° Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all of the many orders of mammals.

  • Higher classification levels are not defined by some measurable characteristic, such as the reproductive isolation that separates biological species.
  • As a result, the larger categories are not comparable between lineages.

° An order of snails does not necessarily exhibit the same degree of morphological or genetic diversity as an order of mammals.

2. Classification and phylogeny are linked.

  • Systematists explore phylogeny by examining various characteristics in living and fossil organisms.
  • They construct branching diagrams called phylogenetic trees to depict their hypotheses about evolutionary relationships.
  • The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups.
  • Methods for tracing phylogeny began with Darwin, who realized the evolutionary implications of Linnaean hierarchy.
  • Darwin introduced phylogenetic systematics in On the Origin of Species when he wrote: “Our classifications will come to be, as far as they can be so made, genealogies.”

    3. Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters.

  • Patterns of shared characteristics can be depicted in a diagram called a cladogram.
  • If shared characteristics are homologous and, thus, explained by common ancestry, then the cladogram forms the basis of a phylogenetic tree.

° A clade is defined as a group of species that includes an ancestral species and all its descendents.

• The study of resemblances among clades is called cladistics. ° Each branch, or clade, can be nested within larger

clades.

• A valid clade is monophyletic, consisting of an ancestral species and all its descendents.

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Classification of Organisms

Notes

  • °  When we lack information about some members of a clade, the result is a paraphyletic grouping that consists of some, but not all, of the descendents.
  • °  The result may also be several polyphyletic groupings that lack a common ancestor.
  • °  Such situations call for further reconstruction to uncover species that tie these groupings together into monophyletic clades.
  • Determining which similarities between species are relevant to grouping the species in a clade is a challenge.
  • It is especially important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy.
  • Systematists must also sort through homologous features, or characters, to separate shared derived characters from shared primitive characters.

    ° A “character” refers to any feature that a particular taxon possesses.

    ° A shared derived character is unique to a particular clade.

    ° A shared primitive character is found not only in the clade being analyzed, but also in older clades.

  • For example, the presence of hair is a good character to distinguish the clade of mammals from other tetrapods.

° It is a shared derived character that uniquely identifies mammals.

• However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals.

° Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates.

• Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.

° The status of a character shared derived versus shared primitive may depend on the level at which the analysis is being performed.

  • A key step in cladistic analysis is outgroup comparison, which is used to differentiate shared primitive characters from shared derived ones.
  • To do this, we need to identify an outgroup, a species or group of species that is closely related to the species that we are studying, but known to be less closely related than any members of the study group are to each other.
  • To study the relationships among an ingroup of five vertebrates (a leopard, a turtle, a salamander, a tuna, and a

Evolution: Taxonomy

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Classification of Organisms

Notes

lamprey) on a cladogram, an animal called the lancelet is a good choice.

° The lancelet is a small member of the Phylum Chordata that lacks a backbone.

  • The species making up the ingroup display a mixture of shared primitive and shared derived characters.
  • In an outgroup analysis, the assumption is that any homologies shared by the ingroup and outgroup are primitive characters that were present in the common ancestor of both groups.
  • Homologies present in some or all of the ingroup taxa are assumed to have evolved after the divergence of the ingroup and outgroup taxa.
  • In our example, a notochord, present in lancelets and in the embryos of the ingroup, is a shared primitive character and, thus, not useful for sorting out relationships between members of the ingroup.
    • °  The presence of a vertebral column, shared by all members of the ingroup but not the outgroup, is a useful character for the whole ingroup.
    • °  The presence of jaws, absent in lampreys and present in the other ingroup taxa, helps to identify the earliest branch in the vertebrate cladogram.
  • Analyzing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.
  • A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.
    • °  However, this chronology does not indicate the time of origin of the species that we are comparing, only the groups to which they belong.
    • °  For example, a particular species in an old group may have evolved more recently than a second species that belongs to a newer group.
  • A cladogram is not a phylogenetic tree.

° To convert it to a phylogenetic tree, we need more information from sources such as the fossil record, which can indicate when and in which groups the characters first appeared.

  • Any chronology represented by the branching pattern of a phylogenetic tree is relative (earlier versus later) rather than absolute (so many millions of years ago).
  • Some kinds of tree diagrams can be used to provide more specific information about timing.

Evolution: Taxonomy

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Classification of Organisms

Notes

  • In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in a lineage.
  • Even though the branches in a phylogram may have different lengths, all the different lineages that descend from a common ancestor have survived for the same number of years.
    • °  Humans and bacteria had a common ancestor that lived more than 3 billion years ago.
    • °  This ancestor was a single-celled prokaryote and was more like a modern bacterium than like a human.
    • °  Even though bacteria have apparently changed little in structure since that common ancestor, there have nonetheless been 3 billion years of evolution in both the bacterial and eukaryotic lineages.
  • These equal amounts of chronological time are represented in an ultrameric tree.
  • In an ultrameric tree, the branching pattern is the same as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal lengths.
  • Ultrameric trees do not contain the information about different evolutionary rates that can be found in phylograms.

° However, they draw on data from the fossil record to place certain branch points in the context of geological time.

4. The principles of maximum parsimony and maximum likelihood help systematists reconstruct phylogeny.

• As available data about DNA sequences increase, it becomes more difficult to draw the phylogenetic tree that best describes evolutionary history.

° If you are analyzing data for 50 species, there are 3 × 1076 different ways to form a tree.

  • According to the principle of maximum parsimony, we look for the simplest explanation that is consistent with the facts.
    • °  In the case of a tree based on morphological characters, the most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters.
    • °  For phylograms based on DNA sequences, the most parsimonious tree requires the fewest base changes in DNA.
  • The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree should reflect the most likely sequence of evolutionary events.

Parsimony

In science, parsimony is to prefer least complicated explanation for an observation. This is generally regarded as good when judging hypotheses. Ockham’s Razor also states this idea

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Classification of Organisms

Notes

° Maximum likelihood methods are designed to use as much information as possible.

  • Many computer programs have been developed to search for trees that are parsimonious and likely:
    • °  “Distance” methods minimize the total of all the percentage differences among all the sequences.
    • °  More complex “character-state” methods minimize the total number of base changes or search for the most likely pattern of base changes among all the sequences.
  • Although we can never be certain precisely which tree truly reflects phylogeny, if they are based on a large amount of accurate data, the various methods usually yield similar trees.

    5. Phylogenetic trees are hypotheses.

• Any phylogenetic tree represents a hypothesis about how the organisms in the tree are related.

° The best hypothesis is the one that best fits all the available data.

• A hypothesis may be modified when new evidence compels systematists to revise their trees.

° Many older phylogenetic hypotheses have been changed or rejected since the introduction of molecular methods for comparing species and tracing phylogeny.

  • Often, in the absence of conflicting information, the most parsimonious tree is also the most likely.

    ° Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious.

    ° Nature does not always take the simplest course.

    ° In some cases, the particular morphological or molecular character we are using to sort taxa actually did evolve multiple times.

  • For example, the most parsimonious assumption would be that the four-chambered heart evolved only once in an ancestor common to birds and mammals but not to lizards, snakes, turtles, and crocodiles.
  • But abundant evidence indicated that birds and mammals evolved from different reptilian ancestors.
    • °  The hearts of birds and mammals develop differently, supporting the hypothesis that they evolved independently.
    • °  The most parsimonious tree is not consistent with the above facts, and must be rejected in favor of a less parsimonious tree.
  • The four-chambered hearts of birds and mammals are analogous, not homologous.

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Classification of Organisms

Notes

• Occasionally misjudging an analogous similarity in morphology or gene sequence as a shared derived homology is less likely to distort a phylogenetic tree if several derived characters define each clade in the tree.

° The strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as by fossil evidence.

6. An organism’s evolutionary history is documented in its genome.

  • Molecular systematics is a valuable tool for tracing an organism’s evolutionary history.
  • The molecular approach helps us to understand phylogenetic relationships that cannot be measured by comparative anatomy and other nonmolecular methods.

° For example, molecular systematics helps us uncover evolutionary relationships between groups that have no grounds for morphological comparison, such as mammals and bacteria.

• Molecular systematics enables scientists to compare genetic divergence within a species.

° Molecular biology has helped to extend systematics to evolutionary relationships far above and below the species level.

  • Its findings are sometimes inconclusive, as in cases where a number of taxa diverged at nearly the same time.
  • The ability of molecular trees to encompass both short and long periods of time is based on the fact that different genes evolve at different rates, even in the same evolutionary lineage.

° For example, the DNA that codes for ribosomal RNA (rRNA) changes relatively slowly, so comparisons of DNA sequences in these genes can be used to sort out relationships between taxa that diverged hundreds of millions of years ago.

• In contrast, mitochondrial DNA (mtDNA) evolved relatively recently and can be used to explore recent evolutionary events, such as relationships between groups within a species.

7. Gene duplication has provided opportunities for evolutionary change.

  • Gene duplication increases the number of genes in the genome, providing opportunities for further evolutionary change.
  • Gene duplication has resulted in gene families, which are groups of related genes within an organism’s genome.

Introns & Exons (grade 10 review)

Introns are sections of DNA within a gene that do not encode part of the protein that the gene produces, and are spliced out of the mRNA that is transcribed from the gene before it is exported from the cell nucleus. Introns exist mainly (but not only) in eukaryotic cells. The regions of a gene that remain in the spliced mRNA are called exons.

Source: Wikipedia

Introns = interruptions in the DNA Exons = expressed DNA code

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Classification of Organisms

Notes

  • Like homologous genes in different species, these duplicated genes have a common genetic ancestor.
  • There are two types of homologous genes: orthologous genes and paralogous genes.
  • The term orthologous refers to homologous genes that are found in different gene pools because of speciation.

° The ß hemoglobin genes in humans and mice are orthologous.

  • Paralogous genes result from gene duplication and are found in more than one copy in the same genome.
    • °  Olfactory receptor genes have undergone many gene duplications in vertebrates.
    • °  Humans and mice each have huge families of more than 1,000 of these paralogous genes.
  • Now that we have compared entire genomes of different organisms, two remarkable facts have emerged.
  • Orthologous genes are widespread and can extend over enormous evolutionary distances.
    • °  Approximately 99% of the genes of humans and mice are demonstrably orthologous, and 50% of human genes are orthologous with those of yeast.
    • °  All living things share many biochemical and development pathways.
  • The number of genes seems not to have increased at the same rate as phenotypic complexity.
    • °  Humans have only five times as many genes as yeast, a simple unicellular eukaryote, although we have a large, complex brain and a body that contains more than 200 different types of tissues.
    • °  Many human genes are more versatile than yeast and can carry out a wide variety of tasks in various body tissues.

      8. Molecular clocks may keep track of evolutionary time.

  • In the past, the timing of evolutionary events has rested primarily on the fossil record.
  • One of the goals of evolutionary biology is to understand the relationship among all living organisms, including those for which there is no fossil record.
  • Molecular clocks serve as yardsticks for measuring the absolute time of evolutionary change.
    • °  They are based on the observation that some regions of the genome evolve at constant rates.
    • °  For these regions, the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the two species last shared a common ancestor.

Homologous genes – genes having similar structures and functions.

Paralogous – two genes or clusters of genes at different chromosomal locations in the same organism that have structural similarities indicating that they derived from a common ancestral gene.

Orthologous – homologous genes that originated through speciation, i.e., genes in different species, that are similar to each other because they originated from a common ancestor (for example, human and mouse, e.g., globin (transport) protein).

Source: Wikipedia

Gene Duplication

Gene duplication occurs when an error in DNA replication leads to the duplication of a region of DNA containing a (generally functional) gene. The significance of this process for evolutionary biology is that if a gene is under natural selection, most mutations will lead to the death of the organism. When a gene is duplicated selection may be removed from one copy and now the other gene locus is free to mutate and discover new functions.

The two genes that exist after a gene duplication event are called paralogs and usually code for proteins with a different function and/or structure. By contrast, orthologous genes are ones which code for proteins with similar functions but exist in different species, and are created from a speciation event.

Source: Wikipedia

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Classification of Organisms

Notes

° In the case of paralogous genes, the number of substitutions is proportional to the time since the genes became duplicated.

  • We can calibrate the molecular clock of a gene by graphing the number of nucleotide differences against the timing of a series of evolutionary branch points that are known from the fossil record.
    • °  The slope of the best line through these points represents the evolution rate of that molecular clock.
    • °  This rate can be used to estimate the absolute date of evolutionary events that have no fossil record.
  • No molecular clock is completely accurate.
    • °  Genes that make good molecular clocks have fairly

      smooth average rates of change.

    • °  No genes mark time with a precise tick-tock accuracy in

      the rate of base changes.

    • °  Over time there may be chance deviations above and below the average rate.
  • Rates of change of various genes vary greatly.

° Some genes evolve a million times faster than others.

  • The molecular clock approach assumes that much of the change in DNA sequences is due to genetic drift and is selectively neutral.
    • °  The neutral theory suggests that much evolutionary change in genes and proteins has no effect on fitness and, therefore, is not influenced by Darwinian selection.
    • °  Researchers supporting this theory point out that many new mutations are harmful and are removed quickly.
    • °  However, if most of the rest are neutral and have little or no effect on fitness, the rate of molecular change should be clocklike in their regularity.
  • Differences in the rates of change of specific genes are a function of the importance of the gene.
    • °  If the exact sequence of amino acids specified by a gene is essential to survival, most mutations will be harmful and will be removed by natural selection.
    • °  If the sequence of genes is less critical, more mutations will be neutral, and mutations will accumulate more rapidly.
  • Some DNA changes are favored by natural selection.

° This leads some scientists to question the accuracy and

utility of molecular clocks for timing evolution.

• Evidence suggests that almost 50% of the amino acid differences in proteins of two Drosophila species have resulted from directional natural selection.

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Classification of Organisms

Notes

• Over very long periods of time, fluctuations in the rate of accumulation of mutations due to natural selection may even out.

° Even genes with irregular clocks can mark elapsed time approximately.

  • Biologists are skeptical of conclusions derived from molecular clocks that have been extrapolated to time spans beyond the calibration in the fossil record
    • °  Few fossils are older than 550 million years old.
    • °  Estimates for evolutionary divergences prior to that time may assume that molecular clocks have been constant over billions of years.
    • °  Such estimates have a high degree of uncertainty.
  • The molecular clock approach has been used to date the jump of the HIV virus from related SIV viruses that infect chimpanzees and other primates to humans.
    • °  The virus has spread to humans more than once.
    • °  The multiple origins of HIV are reflected in the variety

      of strains of the virus.

  • HIV-1 M is the most common HIV strain.
    • °  Investigators have calibrated the molecular clock for the virus by comparing samples of the virus collected at various times.
    • °  From their analysis, they project that the HIV-1 M strain invaded humans in the 1930s.

      9. There is a universal tree of life.

• The genetic code is universal in all forms of life.
° From this, researchers infer that all living things have a

common ancestor.

  • Researchers are working to link all organisms into a universal tree of life.
  • Two criteria identify regions of DNA that can be used to reconstruct the branching pattern of this tree.
    • °  The regions must be able to be sequenced.
    • °  They must have evolved slowly, so that even distantly related organisms show evidence of homologies in these regions.
  • rRNA genes, coding for the RNA component of ribosomes, meet these criteria.
  • Two points have emerged from this effort:

1. The tree of life consists of three great domains: Bacteria,

Archaea, and Eukarya.

° Most prokaryotes belong to Bacteria.

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Classification of Organisms

  • °  Archaea includes a diverse group of prokaryotes that inhabit many different habitats.
  • °  Eukarya includes all organisms with true nuclei, including many unicellular organisms as well as the multicellular kingdoms.

2. The early history of these domains is not yet clear.

  • °  Early in the history of life, there were many interchanges

    of genes between organisms in the different domains.

  • °  One mechanism for these interchanges was horizontal gene transfer, in which genes are transferred from one genome to another by mechanisms such as transposable elements.
  • °  Different organisms fused to produce new, hybrid organisms.
  • °  It is likely that the first eukaryote arose through fusion between an ancestral bacterium and an ancestral archaean.

Horizontal gene transfer –
hinders clarification of the deepest branchings in a phylogenetic tree that depicts the origins of the three domains.

Source:
Biology 7th ed, Campbell Joan Sharp, SFU

Notes

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Biology 11 Review Notes

Classification of Organisms Appendix See Chapter 17

Vocabulary List for Chapter 17 – Classification of Organisms

B
 binomial nomenclature  blastopore
 blastula

C
 cladistics  cladogram  class

D
 derived character  division
 domain
 domain Archaea

 domain Bacteria  domain Eukarya

E
 echinoderm  eubacteria

F
 family

G
 genus

K
 kingdom  kingdom  kingdom  kingdom  kingdom

 kingdom  kingdom

Animalia Archaebacteria Eubacteria Fungi

Plantae Protista

O
 order

P
 phylogenetic tree  phylogeny
 phylum
 protist

S
 species
 species identifier  species name
 subspecies
 systematics

T
 taxonomy

V
 variety

Some of these terms are used for the online Crossword review.

Evolution: Taxonomy 15

Classification of Organisms Appendix

Vocabulary List by Topic (with additional terms)

Overview

Phyogeny and Systematics  phylogeny
 systematics,
 molecular systematics,

A. Phylogenies Are Based on Common Ancestries

1. Sedimentary rocks are the richest source of fossils.

fossil record

2. Morphological and molecular similarities may provide clues to phylogeny.
 analogy.
 homoplasies.

B. Phylogenetic Systematics: Connecting Classification with Evolutionary History

1. Taxonomy employs a hierarchical system of classification.
 binomial.
 genus,

 specific epithet,
 species
 hierarchical classification
 family, order, class, phylum, kingdom,  domain.
 taxon.

2. Classification and phylogeny are linked.

Etymologies

3. Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters.
 clade
 cladistics.

 monophyletic,
 paraphyletic
 polyphyletic
 shared derived character  shared primitive character  outgroup,

 ingroup
 phylogram,
 ultrameric tree.

4. The principles of maximum parsimony and maximum likelihood help systematists reconstruct phylogeny.
 maximum parsimony,

 maximum likelihood
5. Phylogenetic trees are hypotheses.

6. An organism’s evolutionary history is documented in its genome.

7. Gene duplication has provided opportunities for evolutionary change.
 orthologous

 Paralogous

8. Molecular clocks may keep track of evolutionary time.
 Molecular clocks
 neutral theory

9. There is a universal tree of life.

analog- = proportion (analogy: similarity due to convergence)

bi- = two; nom- = name (binomial: a two-part latinized name of a species)

clado- = branch (cladogram: a dichotomous phylogenetic tree that branches repeatedly)

homo- = like, resembling (homology: similarity in characteristics resulting from a shared ancestry)

mono- = one (monophyletic: pertaining to a taxon derived from a single ancestral species that gave rise to no species in any other taxa)

parsi- = few (principle of parsimony: the premise that a theory about nature should be the simplest explanation that is consistent with the facts)

phylo- = tribe; -geny = origin (phylogeny: the evolutionary history of a taxon)

Evolution: Taxonomy 16

Classification of Organisms Appendix

Evolution: Taxonomy 17

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes and have No Comments
06
Jul

Bio 11 SS Lesson 2 Wed

Biology 11 Lesson Outline                                      Date July 6th

 

 

Last lessons Objectives

 

 

  

 

·      Life in “Gunner Bio”

·      What is biology (see concept map)

·      Observe and then what?

 Evaluation
Today’s Objectives 1.   Why classify to understand Unity and Diversity

https://en.wikibooks.org/wiki/General_Biology/Classification_of_Living_Things/Classification_and_Domains_of_Life

 

2.   How do you organize billions of species?

http://www.slideshare.net/coachpointer/taxonomy-ppt-11592335

 

3.   How is classification linked to evolution?

http://evolution.berkeley.edu/evolibrary/article/evo_10

 

  
Topic

Number One

 8-9

 

·      Rewake (Yesterday’s Red Flags)

·      Recap

·      Today’s Mission

 

Inquiry questions

Classification and Taxonomy

·      How is taxonomy organized?

·      What is the significance of a bionomial systems?

·      Two types of classification techniques.

 

The original idea by Linnaeus was to make phylogenic tree, using a pattern of smallest to greatest similarity.

This idea did not consider evolutionary relationships between classified species.

How to make a dichotomous key

https://www.youtube.com/watch?v=YDGv_n_11qs

 

https://www.youtube.com/watch?v=1NnUIYro4LY

 

Leaf Lab: Using a guide to classify a sample leaf.

 

Reference

 

http://www.ext.colostate.edu/mg/gardennotes/122.html

 

 

Activity time: approx. 30 minutes

 

  
Topic

Number Two

 9-10

Initial Problem to solve

Power point

DNA and Classification

 

http://evolution.berkeley.edu/evolibrary/article/phylogenetics_02

 

Key Concept:

 

In class:

http://evolution.about.com/od/Microevolution/a/Dna-And-Evolution.htm

 

DNA Evolution

http://www.exploredna.co.uk/evolution-dna.html

 

http://evolution.berkeley.edu/evolibrary/article/mutations_01

 

 

Organisms are now classified that show lines of evolutionary descent.

 

Molecular similarities in DNA provide clues to similar species. (See case study). If a species has the same DNA how closely do you think the two species are?

 

A gene, is a segment of DNA. DNA is a code to produce proteins. Similarity in proteins can be used to classify organisms at a molecular level.

 

Classification of Insects

Using sample jar to classify insects.

Using Bio Lab Book

 

Another class activity

 

Reference Activity

http://www.bu.edu/gk12/eric/cladogram.pdf

 

 

  
Topic

Number Three

 11

Quiz

Chapter Two

·      Evidence of Evolution

·      Direct and Indirect evidence

·      Trouble with fossils

·      4 Types of indirect Evidence

 

Case study: Chapter Two Horses

 

 

  
Debrief and new topic 11-11:43

 

So far

·      Observe

·      Classify

·      Experiment

·      Theory

 

  
Text Book

 

Class Notes

 Chapter One: Refer to online for focal points.

Chapter one Taxonomy

Just Taxonomy and not Viruses

 

 

  
     
You tube Reference Crash course

https://www.youtube.com/watch?v=F38BmgPcZ_I

 

Amoeba Sisters

https://www.youtube.com/watch?v=wpKulkADzBk

 

Bill Nye: Evolution

https://www.youtube.com/watch?v=JZodeVvhjmE

 

Quizlet

https://quizlet.com/12555289/prentice-hall-biology-chapter-18-classification-key-concepts-flash-cards/

 

Prentice Hall

https://www.youtube.com/watch?v=JAm4v0K-qc8

 

  
Vocab Taxonomy                     evolutionary classification

Binomial nomenclature   Cladogram

Kingdom                       domain

Phylum                         Eubacteria

Class                            Archeobacteria

Order

Family

Genus

Species

  
Take Home Message “Comparisons can be Odious” Jack Keroac

yet

Classification is arduous

 

Natural bodies are divided into three kingdomes of nature: viz. the mineral, vegetable, and animal kingdoms. Minerals grow, Plants grow and live, Animals grow, live, and have feeling.

— Carolus Linnaeus
posted by Marc Bernard Carmichael in Science 10 and have No Comments
06
Jul

Bio 11 SS Lesson Two ( July 6)

Biology 11 Lesson Outline                                      Date July 6th

 

 

Last lessons Objectives

 

 

  

 

·      Life in “Gunner Bio”

·      What is biology (see concept map)

·      Observe and then what?

 Evaluation
Today’s Objectives 1.   Why classify to understand Unity and Diversity

https://en.wikibooks.org/wiki/General_Biology/Classification_of_Living_Things/Classification_and_Domains_of_Life

 

2.   How do you organize billions of species?

http://www.slideshare.net/coachpointer/taxonomy-ppt-11592335

 

3.   How is classification linked to evolution?

http://evolution.berkeley.edu/evolibrary/article/evo_10

 

  
Topic

Number One

 8-9

 

·      Rewake (Yesterday’s Red Flags)

·      Recap

·      Today’s Mission

 

Inquiry questions

Classification and Taxonomy

·      How is taxonomy organized?

·      What is the significance of a bionomial systems?

·      Two types of classification techniques.

 

The original idea by Linnaeus was to make phylogenic tree, using a pattern of smallest to greatest similarity.

This idea did not consider evolutionary relationships between classified species.

How to make a dichotomous key

https://www.youtube.com/watch?v=YDGv_n_11qs

 

https://www.youtube.com/watch?v=1NnUIYro4LY

 

Leaf Lab: Using a guide to classify a sample leaf.

 

Reference

 

http://www.ext.colostate.edu/mg/gardennotes/122.html

 

 

Activity time: approx. 30 minutes

 

  
Topic

Number Two

 9-10

Initial Problem to solve

Power point

DNA and Classification

 

http://evolution.berkeley.edu/evolibrary/article/phylogenetics_02

 

Key Concept:

 

Organisms are now classified that show lines of evolutionary descent.

 

Molecular similarities in DNA provide clues to similar species. (See case study). If a species has the same DNA how closely do you think the two species are?

 

A gene, is a segment of DNA. DNA is a code to produce proteins. Similarity in proteins can be used to classify organisms at a molecular level.

 

Classification of Insects

Using sample jar to classify insects.

Using Bio Lab Book

 

Reference Activity

http://www.bu.edu/gk12/eric/cladogram.pdf

 

 

  
Topic

Number Three

 10-11

Quiz

Chapter Two

·      Evidence of Evolution

·      Direct and Indirect evidence

·      Trouble with fossils

·      4 Types of indirect Evidence

 

Case study: Chapter Two Horses

 

 

  
Debrief and new topic 11-11:43

 

Observe

Classify

Experiment

Theory

 

  
Text Book

 

Class Notes

 Chapter One: Refer to online for focal points.

Chapter one Taxonomy

Just Taxonomy and not Viruses

 

 

  
     
You tube Reference Crash course

https://www.youtube.com/watch?v=F38BmgPcZ_I

 

Amoeba Sisters

https://www.youtube.com/watch?v=wpKulkADzBk

 

Bill Nye: Evolution

https://www.youtube.com/watch?v=JZodeVvhjmE

 

Quizlet

https://quizlet.com/12555289/prentice-hall-biology-chapter-18-classification-key-concepts-flash-cards/

 

Prentice Hall

https://www.youtube.com/watch?v=JAm4v0K-qc8

 

  
Vocab Taxonomy                     evolutionary classification

Binomial nomenclature   Cladogram

Kingdom                       domain

Phylum                         Eubacteria

Class                            Archeobacteria

Order

Family

Genus

Species

  
Take Home Message “Comparisons can be Odious” Jack Keroac

yet

Classification is arduous

 

Natural bodies are divided into three kingdomes of nature: viz. the mineral, vegetable, and animal kingdoms. Minerals grow, Plants grow and live, Animals grow, live, and have feeling.

— Carolus Linnaeus
posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Lesson Outline and have No Comments
04
Jul

Biology 11 Lesson Plan July 5

Biology 11 Lesson Outline                                      Date July 5th

 

 

Last lessons Objectives

 

 

  

Ah..last day of regular school.

 Evaluation
Today’s Objectives 1.   This is my classroom and getting squared away.

2.   In and out of class resources

3.   Note topics on the board. What is the significance of the number three?
Topic

Number One

 Congradulations…you have now signed up for PG Gunner School.

 

You are now part of an elite group of individuals attempting to achieve something that several do not achieve during a 8 month program.

There are three basic concepts:

·      Honour

·      Courage

·      Commitment

These are not buzzwords, nor are they something to take lightly. These words are corp principles to keep this class moving.

 

Please note:

Seating arrangement.

Class outline on board

Table tops

Live animals

 
Topic

Number Two

 What is biology.

 

Enclosed at my web blog is a comprehensive outline of topics to read. You are accountable for reading and being prepared to be tested on posted material.

 

Never, read any thing less that five times.

1.   Scan and outline

2.   Record new vocab and make cue card or file.

3.   Separate content into actions and concepts.

4.   Read and fill in gapnotes or make your own gap notes.

5.   Find an online evaluation to confirm you are proficient in explaining content.

 
Topic

Number Three

  

Test one outline of learning outcomes:

1.   Activities of life

2.   Big ideas of life

3.   Levels of organization

4.   Molecules of life

5.   Scientific method

6.   Origins for biological terms

 
Text Book

 

Class Notes

 Chapter One: Refer to online for focal points.

Chapter one Taxonomy

Just Taxonomy and not Viruses

 

 
You tube Reference How to study biology

https://www.examtime.com/blog/how-to-study-biology/

 

Wikistudy

http://www.wikihow.com/Study-for-Biology

 

Gunner Tips

http://biology.about.com/od/biologyhomeworkhelp/a/aa120705a.htm

 

https://www.butte.edu/cas/tipsheets/studystrategies/studybio.html

 

Gunner Song

https://www.youtube.com/watch?v=Mrlnh3vebSc

 

 

How to write Cornell Notes

https://www.youtube.com/watch?v=WtW9IyE04OQ

 

 
Take Home Message Your motto for the next five weeks

 

“Adapt or Die”

 

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Lesson Outline and have No Comments
04
Jul

Bio 11 SS Word Assignment

Senior Biology

Mr MBK Carmichael

Name: ____________________ Date: __________ Block: _____

 

Word Dissections

Use the table of prefixes and suffixes to complete the two worksheets that follow. Note: some of the words in the list can be used as both a prefix and a suffix

 


PREFIXES

a, an – without, lacking

ad – toward

amphi – two, both

ana – up, up against

anti – opposite

arch – ancient

arthro – jointed

auto – self, same

bi, bin – twice

bio – life

blast, blasto – sprout

bronch, broncho – windpipe

cardio – heart

carne, carni – flesh, meat

chloro – green

chrome, chromo – colour

co, con – with, together

coni – dust

cranio – skull

cyte, cyto – cell

de – away, remove

derm, dermis – layer, skin

di – two, twice

dia – across, through

diplo – double, two

eco – house, environment

ecto – outside, outer

en – in, into

endo – within

epi – amoung

eu – good, true

ex, exo – out, away from

extra – outside, beyond

gastro – stomach

 

gen – race, origin

geo – earth

hema, hemo – blood

herbi – plants

hetero – different

homo, homeo – same

hydro – water

hyper – over, above

hypo – under, below

inter – between

intra – inside

iso – equal

karyo – seed, kernal

leuco, leuko – white

macro, mega – large

micro – small

neuro – nerve

oo – egg

osteo – bone

para – beside

path, patho – disease

peri – around

photo – light

phyll – leaf

pneum, pneumono – lung

poly – many

pro, proto – before

pseudo – false

scope – to look

silico -silicon, quartz

sym, syn – together

therm, thermo – heat

taxis – arrangement

tox – poison

xyl, xylo – wood

zo, zoon – animal

zoa – animals

zyg – yolk or union

 

 

SUFFIXES

cide – killer, murder

cycle – circle

emia – blood

esis – action, process

fer – bearing fruit

gram – draw, record

graph – write, record

itis – inflammation

kinesis – movement

logy – study of

lysis – loosen, split

mer, mere – part

meter – measure

nomy – method

oma – swelling

osis – condition, disease

ous – characterized by

philic – love

plasm – mold, form

pod – foot

rrhea – flowing

septic – infected

some – of the body

stasis – stand, stop

stome – mouth

tom, tomy – to cut

trophy – nutrition

trop, tropy – move towards

vore, vorous – eater

y – quality of

 



Word Dissections

Worksheet 1 – Literal Meanings

Fill in the prefixes and suffixes for the following science terms.

 

  1. cardiogram = heart + record

 

 

  1. antiseptic ____________ + _____________
  2. xylotomy ____________ + _____________
  3. oocyte ____________ + _____________
  4. arthritis ____________ + _____________
  5. microtome ____________ + _____________
  6. chromosome ____________ + _____________
  7. blastogenesis ____________ + _____________ + _____________
  8. arthropod ____________ + _____________
  9. isomer ____________ + _____________
  10. thermograph ____________ + _____________
  11. ectoderm ____________ + _____________
  12. bronchitis ____________ + _____________
  13. leukocyte ____________ + _____________
  14. toxemia ____________ + _____________
  15. chlorophyll ____________ + _____________
  16. neurology ____________ + _____________
  17. biogeography ____________ + _____________ + ______________
  18. photochrome ____________ + _____________
  19. isothermal ____________ + _____________
  20. atom ____________ + _____________

 

 

 

 

Word Dissections

Worksheet 2 – Actual Meanings

Match the following science terms with their definitions.

Use Worksheet 1 to help you choose the correct answers.

 

eg: cardiogram = a graphical recording of a heartbeat

 

 

____ 1.    antiseptic                a) film that darkens when exposed to light

____ 2.   xylotomy                  b) a type of asexual reproduction

____ 3.   oocyte                     c) preparing wood for microscopic examination

____ 4.   arthritis                  d) a green pigment in plants cells

____ 5.   microtome                e) the prevention of infection

____ 6.   chromosome              f) tiny particle of matter, once thought to be                                                     indivisible

____ 7.   blastogenesis            g) animal with jointed legs and an exoskeleton

____ 8.   arthropod                 h) of constant temperature

____ 9.   isomer                     i)   the study of the nervous system

____ 10. thermograph             j) an egg cell

____ 11.   ectoderm                  k) chemical compounds composed of the same elements

____ 12. bronchititis              l)   painful inflammation of skeletal joints

____ 13. leukocyte                 m) a thermometer for recording variations in                                                       temperature

____ 14. toxemia                    n) white blood cells

____ 15. chlorophyll               o) a darkly staining structure found in the nucleus of a                                        cell

____ 16. neurology                 p) poisonous substances in the blood

____ 17. biogeography             q) outer layer of cells that forms the skin

____ 18. photochrome             r) branch of biology that deals with the distribution                                            of life forms around the world

____ 19. isothermal                s) inflammation of the breathing tubes

____ 20. atom                        t) a precision instrument for cutting thin sections of                                          tissue for microscopic examination

 

 

 

 

 

 

 

 

Word Dissections

Worksheet 3 – Making Words

Using your prefix-suffix list, write the biological term for each of the following.

 

eg:   A bacteria killer – “-cide” means killer, so the term would be “bactericide”.

 

 

  1. White cell = _________________________________

 

  1. Outside skeleton = _________________________________

 

  1. Middle layer of the leaf       = _________________________________

 

  1. Outside of the cell = _________________________________

 

  1. Study of animals   = _________________________________

 

  1. Study of form = _________________________________

 

  1. A one-celled organism = _________________________________

 

  1. A term describing an organism made up of many cells = __________________________

 

  1. Green leaf = _________________________________

 

  1. Person that studies cells       = _________________________________

 

 

 

 

 

 

 

 

 

 

 

 

 

posted by Marc Bernard Carmichael in Science 10 and have No Comments
04
Jul

Bio 11 Day 1 Summer School

Welcome to my blog.

Today’s introductory file will the the largest file.

Enclosed in today’s lesson notes will be the following:

Topic One: Art of Observation

How observant are you and how can you improve your skills regarding observation? Notice and look for clues. Can you measure something or use qualitative properties. As you observe, are you attempting to just sense what is in front of you verses wondering who may be calling you on your phone.

Refer to you classmates on this activity.

For further inspiration go to:

http://lifehacker.com/5960811/how-to-develop-sherlock-holmes-like-powers-of-observation-and-deduction

The mission  that you have chosen is simple and yet challenging.

In less than five weeks, you are attempting to learn and be accountable for a complete year’s course content. The following are the PLO’s and the amount of time usually prescribed for a full year course.

Topic two. BIOLOGY 11 – PROSCRIBED LEARNING OUTCOMES

It is expected that students will:

 

Processes of science

A1 demonstrate safe and correct technique for a variety of laboratory procedures

A2 design an experiment using the scientific method

A3 interpret data from a variety of text and visual sources

Taxonomy (3-5 hours) 2-4 classes

B1 apply the Kingdom system of classification to study the diversity of organisms

Evolution (5-10 hours) 4-6 classes

C1 describe the process of evolution

Ecology (10-12 hours) 6-8 classes

D1 analyse the functional inter-relationships of organisms within an ecosystem

Microbiology (20-25 hours) 13-16 classes

Viruses

E1 evaluate the evidence used to classify viruses as living or non-living

E2 evaluate the effects of viruses on human health

Kingdom Monera

E3 analyse monerans as a lifeform at the prokaryotic level of organization

E4 evaluate the effectiveness of various antibiotics, disinfectants, or antiseptics on bacterial cultures

Plant Biology (20-23 hours) 13-15 classes

F1 analyse how the increasing complexity of algae, mosses, and ferns represent an evolutionary continuum of adaptation to a land environment

F2 analyse how the increasing complexity of gymnosperms and angiosperms contribute to survival in a land environment

Animal Biology (32-35 hours) 22-24 classes

G1 analyse how the increasing complexity of animal phyla represents an evolutionary continuum

G2 analyse the increasing complexity of the Phylum Porifera and the Phylum Cnidaria

G3 analyse the increasing complexity of the Phylum Platyhelminthes, the Phylum Nematoda, and the Phylum Annelida

G4 analyse the increasing complexity of the Phylum Mollusca, the Phylum Echinodermata, and the Phylum Arthropoda

G5 relate the complexity of the form and function of vertebrates to the evolutionary continuum of animals

 

Class Protocol and Time line

Biology 11

Mr MBK Carmiichael Room 411

BIOLOGY 11

Policies and Expectations

Welcome to Summer School Biology 11. This course is only for people who are willing to work at an extremely accelerated rate. We will be completing one week’s worth of work EVERY DAY! This means tests every other day, 2 or more hours of homework daily and withdrawal for poor attendance. If you have failed Biology 11 before, I advise you not to take this course. People who have failed rarely obtain a mark higher than a pass. If you received lower than a C+ in Science 10, you will also have a difficult time working at this accelerated pace. It is very difficult to obtain an A in summer school. If you are not entirely committed to working on this course your chances of success are slim.

As your teacher, I will only be available during class time. Unlike regular school sessions, when the class ends, so does my teaching time. If you need to ask any questions, class time is the time to ask them.

I repeat, I leave the same time that you do.

Materials

Unless told otherwise, bring the following materials to EVERY class:

  • your textbook
  • your blue/black pen, pencil, eraser and ruler
  • your three-ringed binder containing:
    • all of the notes and assignments you have done to date
    • at least 20 pages of punched lined paper
    • at least 10 pages of punched unlined paper

If you don’t bring the necessary materials to class, you cannot do the required work. Do not expect to borrow materials from your teacher or your fellow classmates. You will be given only one copy of each handout, they will not be replaced! Make sure you have received all handouts before you leave the classroom or at the beginning of the period if you were absent the previous period. Assignments or parts of assignments not completed with the excuse “I didn’t get one” will not be given marks.

Attendance

Regular attendance is expected. One class in summer school is equivalent to one weeks worth of classes in day school. For this reason, the summer school policy is for expulsion after 2 absences with no refund. Lates are also recorded and count as a half day absence.

Attendance will be taken immediately after the bell. You are expected to be in your seats with your materials ready by this time. You may be marked away if you are not in the classroom or in your seat when attendance is taken. Doctors, dentists and other appointments are not excuses for missing class. If you are serious about this course you will schedule your appointments around it.

 

Assignments and Tests

Homework assignments will be given daily. In most cases, class time will be given to at least begin the assignment. If you do not understand any aspect of the assignment, ask for an explanation before you leave the class. Assignments are due at the beginning of the next period. An assignment is considered late if it is not handed in with the rest of the class assignments and will be deducted 1/3 of the total possible marks. Late assignments will be accepted only until the end of the break the day they are due.

On average you will be tested every two days. You will be tested the next day on material just covered. For this reason it is very important that you follow along with the work in class. If you do not review the material daily and complete all the homework you will do poorly. Unless told otherwise, all your assignments must be completed in blue or black ink. Your assignments must be neat and all papers longer than one page must be stapled together. Any assignment folded, ripped out of the binder, not completed in ink, not stapled or otherwise mutilated must be resubmitted and will be accordingly marked late. Any paper turned in without a name will receive a zero.

Grading

The overall final letter grade will be a combination of the classroom mark (80%) and the final exam (20%). The classroom mark consists of test and quizzes (70%), labs (20%) and homework assignments (10%). Notice for quizzes may or may not be given, but at least one day’s notice will be given for each test. If you are away or late the day of quiz, test, lab or any other mark, you will receive a mark of zero. You will NOT be able to make up the mark. An interim report indicating your progress will be sent home after 3 weeks. You will not be able to increase your mark through extra work or projects. The only way to boost your overall final mark is to do well on the final exam.

Letter grades:

A     86-100%

B     73-85%

C+   67-72%

C     60-66%

C-   50-59%

F     0-49%

Topic Three: Tenative Course Outline:

 

Date Topic Chapter
July 5 The Nature of Science, Science of Nature

Taxonomy and classification

Levels of organization

 1
July 6 Evolution – The role of DNA 1 and 2

 
July 7 Evolution – Adaptation and Change

Intro Quiz

 2
July 8 Evolution – Theories to Explain Variation 3
     
July 11 Exam One,

Microbiology – Microscopes

 1
July 12 Microbiology – Viruses 7
July 13 Microbiology – Bacteria 8
July 14 Micro Exam, Plants – Intro to Plants and Green Algae 9
July 15 Plants – Mosses and Ferns 10
     
July 18 Plants – Seed Plants 10
July 19 Plants – Plant Structure and Function 11
July 20 Plant Exam: Animals – Intro to animals, Sponges and Cnidarians 12
July 21 Animals – Worms 12
July 22 Animals – Worms and worm dissection 13
     
July 25 Animals – Molluscs, Arthropods and Echinoderms 13
July 26 Animals – Invertebrate chordates and Fish 14
July 27 Animals – Amphibians and reptiles 14
July 28 Animals – Birds and mammals 14
July 29 Animal Exam: Intro to Ecology 16
     
August 2 Ecology: Energy and Ecosystems 16
August 3 Ecology: Cycles and Systems  
August 4 Ecology – Populations and communities 20
August 5 Final Exam

 

To explain what you observe you need both a unique set of terms and a protocol to convert observations into a path towards scientific inquiry.

 

Name: ____________________ Date: __________ Block: _____

 

 

Topic Four : Sample of learning about Biology Word Dissections

Do you know what hematopoiesis is?

Biology can be filled with words that can be difficult to comprehend. By knowing the meanings of common biology prefixes and suffixes, complex biology words will be easier to understand. By “dissecting” these words into discrete units, even the most complex terms can be understood. To demonstrate this concept, let’s begin by performing a biology word dissection on the word above.

The word hematopoiesis contains hemato- (blood) and -poiesis (formation). Therefore, Hematopoiesis is the formation of blood or blood cells.

What about Pneumonoultramicroscopicsilicovolcanoconiosis?

Yes, this is an actual word. What does it mean?

To perform this biology word dissection, we’ll need to proceed carefully. First, we come to the prefix pneumo- which means lung. Next, is ultra, meaning extreme, and microscopic, meaning small. Now we come to silico-, which refers to silicon, and volcano which refers to the mineral particles that make up a volcano. Then we have coni-, a derivative of the Greek word “konis” meaning dust. Finally, we have the suffix -osis which means affected with. Now lets rebuild what we have dissected:

Considering the prefix pneumo- and the suffix -osis, we can determine that the lungs are affected with something. But what? Breaking down the rest of the terms we get extremely small (ultramicroscopic) silicon (silico-) and volcanic (volcano-) dust (coni-) particles. Thus, pneumonoultramicroscopicsilicovolcanoconiosis is a disease of the lungs resulting from the inhalation of very fine silicate or quartz dust. That wasn’t so difficult, now was it?

Now that we’ve honed our dissection skills, let’s try some frequently used biology terms.

Arthritis

(Arth-) refers to joints and (-itis) means inflammation. Arthritis is the inflammation of a joint(s).

Erythrocyte

(Erythro-) means red and (-cyte) means cell. Erythrocytes are red blood cells.

Okay, let’s move on to more difficult words. For instance:

 

Electroencephalogram

Dissecting, we have (electro-), pertaining to electricity, (encephal-) meaning brain, and (-gram) meaning record. Together we have an electric brain record or EEG. Thus, we have a record of brain wave activity using electrical contacts.

Schizophrenia

Individuals with this disorder suffer from delusions and hallucinations. (Schis-) means split and (phren-) means mind.

Thermoacidophiles

These are ancient bacteria that live in extremely hot and acidic environments. (Therm-) means heat, next you have (-acid), and finally (phil-) means love. Together we have heat and acid lovers.

Once you understand the commonly used prefixes and suffixes, obtuse words are a piece of cake! Now that you know how to apply the word dissection technique, I’m sure you’ll be able to determine the meaning of the word thigmotropism (thigmo – tropism).

One of the keys to being successful in biology is being able to understand the terminology. Difficult biology words and terms can be made easy to understand by becoming familiar with common prefixes and suffixes used in biology. These affixes, derived from Latin and Greek roots, form the basis for many difficult biology words.

Below is a list of a few biology words and terms that many biology students find difficult to understand. By breaking these words down into discrete units, even the most complex terms can be understood.

  1. Autotroph

This word can be separated as follows: Auto – troph.

Auto – means self, troph – means nourish. Autotrophs are organisms capable of self nourishment.

  1. Cytokinesis

This word can be separated as follows: Cyto – kinesis.

Cyto – means cell, kinesis – means movement. Cytokinesis refers to the movement of the cytoplasm that produces distinct daughter cells during cell division.

  1. Eukaryote

This word can be separated as follows: Eu – karyo – te.

Eu – means true, karyo – means nucleus. A eukaryote is an organism whose cells contain a “true” membrane bound nucleus.

  1. Heterozygous

This word can be separated as follows: Hetero – zyg – ous.

Hetero – means different, zyg – means yolk or union, ous – means characterized by or full of. Heterozygous refers to a union characterized by the joining of two different alleles for a given trait.

  1. Hydrophilic

This word can be separated as follows: Hydro – philic.

Hydro – refers to water, philic – means love. Hydrophilic means water-loving.

  1. Oligosaccharide

This word can be separated as follows: Oligo – saccharide.

Oligo – means few or little, saccharide – means sugar. An oligosaccharide is a carbohydrate that contains a small number of component sugars.

  1. Osteoblast

This word can be separated as follows: Osteo – blast.

Osteo – means bone, blast – means bud or germ (early form of an organism). An osteoblast is a cell from which bone is derived.

  1. Tegmentum

This word can be separated as follows: Teg – ment – um.

Teg – means cover, ment – refers to mind or brain. The tegmentum is the bundle of fibers that cover the brain.

 

Topic Five: Path to Scientific Inquiry

The Scientific Method

Lets start with some Definitions

 

1) Fact = an observation that has been repeatedly confirmed

eg: normal human body cells have 23 pairs of chromosomes

2) Law = a description of a pattern or a relationship. A generalization based on observations.

eg: the Law of Gravity

3) Hypothesis = a suggested explanation for a phenomenon.

eg: the One gene-one enzyme Hypothesis

4) Scientific Theory = a concept that joins together many related facts, laws and hypotheses that have been extensively tested and always found to be the best explanation for some phenomena. Note: not the same as in ordinary speech, where a theory = a speculative idea

eg: the Theory of Natural Selection

5) Model = A model is a simplified representation of a complex object or system.

eg: model of a cell

 

 

Topic Six: Unifying Principles of biology

  • Cell Theory – Cells are the fundamental unit of life
  • Evolution – populations of organisms change genetically and irreversibly through time.
  • Gene theory – Genes are the basic unit of heredity
  • Homeostasis – An organism will regulate its internal environment to maintain a stable and constant condition
  • Living organisms consume and transform energy.

 

  1. SOME FORMS OF SCIENTIFIC KNOWLEDGE

 

FACT: a confirmed or, at least, agreed-upon empirical observation (or conclusion if referring to an “inferred” fact).

 

Scientific facts, even what appear to be simple observations, are themselves embedded in or rooted in the theories the observer holds.

 

HYPOTHESIS: a proposed explanation of certain “facts” that must be empirically testable in some conceivable fashion. (Plural: “hypotheses.”)

 

A scientific hypothesis is really not proven true or correct; rather, it is either rejected (or “falsified”) because it is determined to be inconsistent with the data, or, if not rejected, regarded as being “provisionally true” and kept as a working hypothesis to be used until found to be faulty in light of new evidence or further testing. Hypotheses that have withstood numerous, rigorous tests and not found to be “false” are often regarded as “facts” since they are effectively beyond rational dispute.

 

THEORY: an integrated, comprehensive explanation of many “facts” and an explanation capable of generating additional hypotheses and testable predictions about the way the natural world looks and works.

 

Scientific theories represent our best efforts to understand and explain a variety of what appear to be interrelated natural phenomena. Examples include the theory of relativity, cell theory, plate tectonics theory (“continental drift”) and the theory of biological evolution through natural selection (“Darwinian” and “neo-Darwinian” theory).

Topic Seven: What is a living thing?

Six Characteristics of Living Things (Organisms)

 

  1. Cells: Living things are made up of small self-contained untis called cells: The cell is the smallest unit of life. Living things may be unicellular, colonial, or multicellular.

 

  1. Reproduction. Living things can produce similar offspring. New organisms are produced either asexually from a single parent organism, or sexually from two parent organisms.

 

  1. Growth and development: Living things grow and develop and eventually die. Growth is the increase in the number and size of cells. Development is the series of changes between conception and death.

 

  1. Energy: Living things obtain energy from their environment, and use that energy to carry out all cell processes (metabolism). Autotrophs use energy from the sun for photosynthesis, to make their own ‘food’ (glucose). Heterotrophs must eat other organisms for this purpose.

 

  1. Response to Stimuli: Living things respond to their environment. Anything in the environment which causes a living thing to react is called a stimulus.

 

  1. Homeostasis: Living things must maintain stable internal conditions in order to remain alive. These conditions include temperature, water content, salt content, and heartbeat. Maintaining homeostasis requires energy.
posted by Marc Bernard Carmichael in Science 10 and have No Comments
14
Jun

Biology 12 June 14th 2016

Biology 12 Lesson Outline                                                 Date: June 14th

 

Last lessons Reproduction Eval

 
Today’s Lesson 1.   Reproduction Exam

2.   Hand in text book

3.   The final “hurrah”

  
Topic 1 I will have your reproduction quiz marked and several exam and several marks regarding to quiz and exam work.  
Topic 2 Please do not forget to bring your text book to class. A replacement book cost over 150 dollars. So..please find your book. I will check text numbers with your book  
Topic 3 A reflective essay on the topic of a badge I found in London, England

“ If your cut corners and you go in circles”

 

Just the other day, I was lucky enough to chat with a previous a student who has now completed three years at McGill University. She shared with me that university is so competitive and yet she refuses to cheat. She said much of my advice as her teacher was just starting to make sense. Now it is your chance to reflect upon the last year and share some of your wisdom about both what you learned in biology and what other lessons may have been translated.

You have two options for this essay.

Plan A

Your mission is to take the quote above and discuss some of the choices you made this year. It is your chance to voice perhaps wise or less than wise decisions. It is a chance to illustrate not only an understanding of how the body maintains balance but also how you attempted to keep balance in class and in life.

 

Now I am more than aware that some students did bend and break the rules. In my way, I have addressed these issues. Now it is your turn to reflect upon the whole notion of cutting corners. You may have watched corners being bent or you may have chosen to bend the rules your self. So this is your chance to voice your perceptions or choices.

 

Plan B

Select a quote that you wish to share about learning about life or studying biology. Using your experience and knowledge gained in Bio 12 and or please share a reflective essay on your experience in class and how it may impact you in the future.

 

In both cases, please organize your thoughts into a six paragraph essay discussing a thesis topic linked to either of the quotes above. This assignment is meant to communicate ideas and thoughts between you and me the teacher. I am hoping that it will be a beneficial experience for you. Do not stress out about grammar and please do not baffle me with B.S. If you want, you can share some wisdom about your new knowledge about your body and how and why you feel this knowledge is either helpful or not. You may want to evaluate some of your choices and be honest with your reflection about your actions. Yes, I do know some corners were cut and so I would appreciate some feedback. Likewise, in the Big picture, small rationalizations do have a ripple affect.

  
Take Home msg

 

 

 “Cheating in school is a form of self-deception. We go to school to learn. We cheat ourselves when we coast on the efforts and scholarship of someone else.

I would prefer even to fail with honor than win by cheating. Sophocles

 

The dream begins with a teacher who believes in you, who tugs and pushes and leads you to the next plateau, sometimes poking you with a sharp stick called ‘truth’. Dan Rather

 

The test of a good teacher is not how many questions he can ask his pupils that they will answer readily, but how many questions he inspires them to ask him which he finds it hard to answer.

–Alice Wellington Rollins

We are what we repeatedly do. Excellence then, is not an act, but a habit.

–       Aristotle

“I’m not a teacher: only a fellow traveler of whom you asked the way. I pointed ahead – ahead of myself as well as you.”

― George Bernard Shaw
posted by Marc Bernard Carmichael in Science 10 and have No Comments
14
Jun

Bio 11 June 14th Lesson

Biology 11 Lesson Outline                    Date June 14 th

 

 

Last lessons Objective

 

  

Mammals and Birds

 Evaluation
Today’s Objectives  

1.   Animal Quiz 2

2.   Endangered Species Assignment

3.   Life Quote Assignment

 
Topic

Number One

  

I will mark the quiz today and you can check with me in tutorial time

 
Topic

Number Two

 Selling an Endanger Species Assignment.

 

At the last minute, a wealth source tells you that they want to fund an endangered species.

 

Your mission is to select a species, find a linked campaign, and explain why the funds should go to you and other campaigns linked to your endangered species!

 

This is an urgent matter.

There is no time for tons of data or research, so stick to the basics.

·      Select a species

·      Find a linked campaign to that species.

·      Find evidence from that campaign or from online research that the species is worthy of protecting.

·      Using you background in biology, consider the following:

a.   Why has your species become endangered?

b.   Can you to big ideas like interaction or Changes with time?

c.    Why is your species the most viable to save?

d.   Are some of your solutions considering a variety of practical and or affordable strategies, such as saving habitat or breeding?

 

Your written section should take no more that 5 minutes to present.

You can use powerpoint or a written document. It should include picture(s) of the species, the species habitat, basic biology about the species and how it became endangered.

 

The second step

You should make your own poster on a legal size piece of paper to show the species, a focus statement, a slogan and other campaigns that are also on board.

 

Do not make a copy of another campaign. You need to have an original name for your campaign. You can use one or several photos. Please cite the source of the photo.

 

 

Next year, PG will select at least one candidate from your class.

Basic take home point..Keep it simple and to the point.

 

 

 

 
Topic

Number Three

  

The cartoonist Charles Schulz once said ““In the Book of Life, The answers aren’t in the back.”

 

Your mission is to find a quote about life that is not on the wall in the classroom.

 

You are to make a sign for your quote.

 

You should find a quote that other students are not using.

 

You are to write a simple essay to explain how this quote about life is linked to this years study about life.

 

You can use two options.

 

·      Option A

Link you quote to four big ideas or activities in life and show how a quote about “ life” is linked to the study of life.

 

·      Option B

Link your quote to personal reflections about your efforts in class and what your are learned linked both to the study of biology and your own journey through grade 11 and Bio 11

 

In your essay you should have six paragraphs.

The first paragraph should include your quote and which option you are choosing. You should propose some form of a thesis statement or the direction which you wish to follow.

 

The four paragraphs should link either to an activity of life or a big idea.

 

The final paragraph should be a conclusion statement linking the previous four paragraphs to your quote on life.

 

There is no need to over think this assignment, to be honest, the purpose of this assignment is to offer to me, your teacher, another vision of what you may have learned this year. You have already been tested on the core material. Now is a chance to reflect upon how this years knowledge may be of merit further down the road.
Text book Reference

 
You tube Reference  

Writing and reflecting in biology

https://www.washington.edu/trends/reflecting-through-short-easy-to-evaluate-writing-assignments/

 

Bio essay examples

http://blog.salvius.org/2011/05/biology-summative-essay.html

 

https://www.utexas.edu/ugs/sites/default/files/bdp/docs/Reflection%20Essay%20Examples.pdf

 

 
Take Home Message “the times that you impress me the most are the times when you don’t even try”

Joni Mitchell
posted by Marc Bernard Carmichael in Science 10 and have No Comments
03
Jun

Science 10 June 3rd 2016

Science 10 Lesson Outline                            Date: June 3rd

 

Last lessons Objectives

 

 Bring Money (4 dollars) for workshop!

Chapt 3 Vocab

 Evaluations

 
Today’s Objective 1.   Chapt 3 MC

2.   Working on “cheat sheet” for Pretest on Tuesday

3. Purple Duotang Contents

 Yes
Topic

Number One

  

Key Points

·      Common questions on multiple choice test are vocabulary based. Many words are not just science terms.
Topic

Number Two

 1.   You will be allowed hand written legal size sheet started in class.

Sheet needs to include concept map from Unit review and cross section diagram.

2. You can use grade 10 exam booklet

 

 Yes
Topic

Number Three

 The following is a list of items for the Duotang

 

Chemistry

1.   Lab on Vinegar and Chalk

2.   Media assignment on Nuclear power

 

Earth Sciences

1.   7 day weather lab assignment

2.   Media assignment on plate tectonics

3.   Problem set worksheets

4.   Energy in the atmosphere and biogeoclimate map hand outs

 

Biology

1.   Media assignment on farming

2.   Media assignment on pollution linked to fashion

3.   Feedback on vegan story (same lesson as fashion)

 

 

Please make sure to read through the blog lessons to confirm that this list is correct.

 

Media assignments due on Tuesday next week

 

Do not take duotangs!

 

  

 
 

 
Video and Youtube

 

BC provincial exams. Note you need to read and sign off for the right to print up the exam. You cannot make multiple copies nor use for other purposes.

https://www.bced.gov.bc.ca/exams/search/searchResults.php

 

 

 
Other stuff! Please not that I have put a page with links to several teacher pages.
Next Class Pretest for Unit and review prior to Unit 1

 
Take Home Message Do not forget!!!!!

Bring 4 dollars to class for workshop

  

·

 

posted by Marc Bernard Carmichael in Science 10,Science Ten Lessons and have No Comments
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