From time to time, lecture notes may appear here

 

Lecture 1a

Science in General

 

1.      Based on your knowledge from other sources, links in the web page, or other sources, review and be prepared to discuss :

          The nature of science and the scientific method

 

The scientific meaning of ‘hypothesis’ and ‘theory’ (note that ‘theory’ as commonly used has a different meaning in science, e.g. the theory of relativity, germ theory, theory of evolution)

 

For a general review check out the web page: http://undsci.berkeley.edu/article/0_0_0/whatisscience_03

(see other links in the course web page)

 

There are misconceptions about what science is and is and isn’t.  See the Berkeley web page: http://undsci.berkeley.edu/teaching/misconceptions.php

 

What constitutes a fair test in science?  Read: http://undsci.berkeley.edu/article/0_0_0/fair_tests_01

 

           What is the nature of ‘proof’?  Is it possible to prove something to be

           true?

 

2.      What is the role of experimentation in science? 

 

3.      How do scientists regard the supernatural?

 

Evolution

 

      1.  Is evolution the same as Darwinism?

 

      2.  Things Darwin didn’t know about:  DNA, continental drift, radiometric 

           dating, archaea, epigenetics, ribozymes, Hox genes to name a few.  Can

           you make a list of 4 or 5 more?

 

4.      What role did Mendel play in Darwin’s understanding of evolution?

 

Natural Selection

 

1.    What is the difference between Natural Selection, Evolution and

Darwinism?

 

 

2.    Darwin’s concept of natural selection can be thought of in terms of 3

observations and 2 deductions:

 

Obs. 1 – All organisms have the potential to increase exponentially in

              population size

 

Obs. 2 – Populations fluctuate over time but never exhibit a  

               trend toward continuous exponential growth

 

Ded . 1 – Nature limits exponential growth by causing mortality (disease,

                starvation, crowding, competition etc)

 

Obs. 3 -  In general, organisms are unique, each varying from other others

in a range of measurable characteristics; many of these 

variations are heritable, i.e.  changes can be passed on to

offspring

 

       Ded. 2 -  Individuals who inherit variations which confer even a slight

                      benefit in survival and reproduction compared to other

                      individuals are more  likely to survive and, and the trait which

                      provided the benefit will be passed on to the next generation

                       (natural selection).  Over time, the favorable trait will increase in

                      the population as alternate – less beneficial – traits decline and

                      disappear.  This is evolution.

 

5.      The only requirements for natural selection are: (1)  the trait under selection must be heritable (2) The trait must provide a benefit which ultimately results in relatively greater lifetime reproductive success than other individuals which do not inherit the trait (3) The organisms bearing the trait must be capable of reproduction

 

      6.  Darwin viewed evolution as occurring by small steps over long time

           periods.  Complex structure could evolve from simpler structures as long

           as each step conferred a fitness benefit, i.e. somewhat greater lifetime

           reproductive success.

 

 

HARDY-WEINBERG

The Hardy-Weinberg law is important because it defines the condition under which no evolution will occur, i.e. under which gene frequencies will remain unchanged from one generation to the next.

Be sure to know what those conditions are (random mating, large population size, not selection, closed population)

Remember the basic formulas:

p2 + 2pq + q2 = 1 and p + q = 1

p = frequency of the dominant allele in the population
q = frequency of the recessive allele in the population
p2 = frequency of homozygous dominant individuals
q2 = freqency of homozygous recessive individuals
2pq = frequency of heterozygous individuals

PROBLEM

Assume that eye color is determined by a single liocus with two alleles. You have sampled a population in which you know that the percentage of blue-eyed individuals [homozygous recessive genotype (aa)] is 36%. Using that 36%, calculate the following:

  1. The frequency of the "aa" genotype.
  2. The frequency of the "a" allele.
  3. The frequency of the "A" allele.
  4. The frequencies of the genotypes "AA" and "Aa."
  5. The frequencies of the two possible phenotypes, i.e. blue eyes or brown eyes, if "A" is completely dominant over "a."

 

Answer

You have sampled a population in which you know that the percentage of the homozygous recessive genotype (aa) is 36%. Using that 36%, calculate the following:

  1. The frequency of the "aa" genotype. Answer: 36%, as given in the problem itself.
  2. The frequency of the "a" allele. Answer: The frequency of aa is 36%, which means that q2 = 0.36. If q2 = 0.36, then q is the square root of 0.36 = 0.6. Since q equals the frequency of the a allele, then the frequency is 60%.
  3. The frequency of the "A" allele. Answer: Since q = 0.6, and p + q = 1, then p = 0.4; the frequency of A is by definition equal to p, so the answer is 40%.
  4. The frequencies of the genotypes "AA" and "Aa." Answer: The frequency of AA is equal to p2, and the frequency of Aa is equal to 2pq. So, using the information above, the frequency of AA is 16% (i.e. p2 is 0.4 x 0.4 = 0.16) and Aa is 48% (2pq = 2 x 0.4 x 0.6 = 0.48).
  5. The frequencies of the two possible phenotypes if "A" is completely dominant over "a." Answers: Because "A" is totally dominate over "a", the dominant phenotype (brown eyes) will show if either the homozygous "AA" or heterozygous "Aa" genotypes occur. The recessive phenotype (blue eyes) is controlled by the homozygous aa genotype. Therefore, the frequency of the dominant phenotype equals the sum of the frequencies of AA and Aa, and the recessive phenotype is simply the frequency of aa. Therefore, the frequency of brown-eyed individuals is 64% and, in the first part of this question above, you have already shown that the recessive frequency is 36%.

 

Check out this web page for other problems is you are interested.

http://www.k-state.edu/parasitology/biology198/hardwein.html

Sex Lecture 1 Lecture Notes

  1. Asexual Reproduction

 

    1. Primitive mode or reproduction – dating back 3.8x106 years – is mitosis

 

a.  Still the primary mode in  viruses, bacteria, unicellular protists, some

     animals and plants (although most protists,  animals and plants  have sexual

    reproduction in addition, i.e. Haploid/Diploid Cycles)

 

b.      Major problems – all individuals are exact genetic copies of parents (with the exception of rare mutants)

 

c.       About 1.5 billion years ago, an alternate form of reproduction appeared in unicellular eukaryotic organisms which allowed exchange of genetic material between similar organisms.

 

(1)    This involved the temporary fusion of two individuals and the

       reciprocal exchange of genetic material – the start of sex

 

(2)    Evolution of meiosis occurred after the evolution of mitosis, i.e

The evolution of linear chromosomes and mitosis was a prerequisite for the evolution of meiosis and sex.

 

  1. Sexual Reproduction

 

In many unicellular protists, life cycles involve an alteration of haploid and diploid stages.

 

            (a).  Both haploid and diploid stages have advantages

            (b).  Prior to the evolution of sex, the diploid condition could have been achieved

                   by duplication of the genome.

 

1.  True sexual reproduction (involving meiotic exchange of gametes) appeared

     first in unicellular Protists (eukaryotes), and probably involved the fusion of

     individual cells, each acting as a gamete.

 

2.  These cells were equal in size (Isogamy)

 

3.  Although originally, any two cells probably could fuse (syngamy), at some

    point early on, it appears that differences in cell surface chemistry evolved

    such that only individuals with different surface cell chemistries would fuse.

    These are called Mating Types

 

            a)  Generally, only two mating types occurs + (or recipient types) and –

                 (or donor types)

 

4.  One possible advantage to the evolution of mating types is to minimize

     inbreeding.

 

            a)  Individuals of the same mating type may be closely related

                 genetically.

 

            b)  Fusion of related individuals is more likely to produce double

                 recessive genotypes in which harmful recessive genes will be

                 expressed.

 

5.  But why just two mating types?  After all, this cuts the number of potential

     mates in a population by half!

 

            a)  The answer my be the advantage of uniparental inheritance of

                 cytoplasmic organelles.

 

b)      Organelles such a mitochondria and chloroplasts are found only in the

      cytoplasm

           

            c)  If organelles were inherited from both gametes, the zygote would

                 contain a mixture of genetically distinct organelles. (Remember, mitochondria

                 and chloroplasts have their own genomes)

 

            d)  This would present the possibility of intracellular competition between

                  organelles.

 

6.  Evidence to support this hypothesis is provided by a group of ciliate protozoa

     (Paramecium)

 

a)      Unlike other protists, Paramecium has multiple mating types.

 

b)      However, Paramecium has a unique mating system called Conjugation, in which cells line up and exchange haploid pronuclei through a small hole.

 

c)      The hole is too small, and too ephemeral, to permit cytoplasmic organelles such as mitochondria from passing through.

 

d)     In other words, Paramecium achieves uniparental inheritance by a different mechanism, and can thus evolve more than two mating types.

 

  1. Anisogamy – In some protists, and in many (but not all)  multicellular eukaryotes,  only a small proportion of cells in the body will be involved in sex – the so called ‘germ  cells’

 

1.  In general, multicellular organisms produce two categories of gametes, small 

     gametes (microgametes = sperm) and large gametes (macrogametes = ova)

 

2.  This condition is called Anisogamy

 

3.      A number of interesting hypotheses exist to explain the evolution of anisosgamy

 

a.       Frequency Dependent Model -  Assume that within a population of sexually-reproducing isogamous invividuals, a mutation for smaller gametes appeared.

b.      The mutant individuals would be able to produce more gametes, fertilize more gametes, and gain a fitness advantage

c.       The mutant allele should begin to spread through the population

d.      However, as the mutant individuals became more common, the probability that small gametes would fertilize other small gametes would increase

e.       These zygotes would have fewer resources that other zygotes, and would be less likely to survive (fitness decrease)

f.       Under these conditions, a mutation in which small gametes fertilized only large gametes (and vice versa) – if it should appear – would be favored by selection

 

4.      An alternate hypothesis – Hurst & Hamilton (1992)

 

a.       As discussed above, since microgametes (sperm) are too small to contain

mitochondria in their cytoplasm,  syngamy between a micro- and macrogamete does not entail the potential problems of mixed mitochondrial lineages in the zygote, i.e. uniparental inheritance of mitochondria is

guaranteed.

 

5.      Global Implications of Anisogamy

 

a.       Evolution of separate male and female strategies to maximize fitness (gender)

b.      Battle of the Sexes

 

Genomic Imprinting and parent-Offspring Conflict

 

1)      In pregnant humans, nutrients required by the fetus travel via spiral arteries in the

placenta.

 

2)      Tissues around these arteries are invaded by cells from the fetus called cyrtotrophoblasts.  These cells affect the arterial wall, thus reducing the mother’s ability to restrict blood flow to the fetus. ( Why would the mother wish to control this flow?)

 

3)  Fetal cells produce Growth Factor II which facilitates the continued proliferation of 

     cyrtotrophoblasts.  Only the paternally-derived copy of the gene for Growth Factor

     II is expressed; not the maternal copy, i.e. the allele contributed by the father

     promotes greater resource flow into the fetus from the mother.  This is an

     example of Genomic Imprinting.  The opposite allele on the maternal

    chromosome has been silenced.

 

4)  Maternal cells around the arteries produce Growth Factor I, which acts to

      neutralize Growth Factor II, thus partially counteracting the effect of Growth

      Factor II

 

 

An interesting evolution-based hypothesis has been suggested that can account for these facts.  The imprinting of the maternal allele may be a consequence of a conflict of interest between the mother and the father/fetus (both of which have a stake).

While it is obvious that the mother has a vested interest in the survival of her fetus, she may need to balance that current interest against  the need to reserve energy and nutrients for future pregnancies. Thus, a mother’s allocation of maternal resources to the fetus may be balanced by the mother’s potential for future offspring, as well as the needs of current offspring.  However – in most species - any future offspring  may have a different father than the current fetus.  Therefore, the father’s gene, inherited in the fetus, should promote the success of the current fetus, even at the expense of the mother, and her future offspring.