quick chap 6 recap!

Natural selection picks the mutated organisms that are best adapted for survival. But the mutations are not the result of purely random mistakes during gene replication. Darwin postulated that mutations are the result of cell reproduction errors, but an alternate theory, set forth in recent times by Barbara McClintock, that holds more water is that we have perhaps evolved to actively mutate our genes when the environment changes, so as to give our offspring a better chance for survival.

Viruses exhibit this behavior, when antigenic drift causes original mutations in a disease. After a solar flare-up in 1917, two deadly smallpox outbreaks killed millions of people. It is possible that the virus strains mutated when they were irradiated. Antigenic shift, when a virus gets new genes from a similar strain of virus, is also a form of survival enhancing mutation. Viruses also have genes that jump around and either copy and paste or cut and paste new sequences around. Scientists are really interested in these jumping genes, and have taken to giving them punny names like Jordan and Evelknievel. We also have “jumping genes.” Scientists think these are former viruses that we have swallowed into our DNA. 97% of our DNA is used for mutational purposes.We are programmed to mutate if we need to. Our DNA is like a smart computer program that seeks input, not just a simple string of commands that occasionally fail at replication. 

From Atoms to Traits

1. Explain the significance of Mendel. 
Darwin originally thought that traits mixed in offspring, but Mendel's pea plant experiments showed that traits are passed down in discreet units. He called them genetic factors, and his results fixed some of the errors in Darwin's hypothesis.  

2. Draw the structure of DNA and who discovered this structure. 

 

top to bottom: Rosalind Franklin, James Watson, Francis Crick. Franklin thought of doing X-ray microscopy, and WC interpreted the results. WC got the Nobel. 

3. Explain each of the five examples of variations that occur to DNA and give an example of each. 
Point Mutation: A base-pair change that can change the functionality of a gene sequence, like whippet dogs with two mutations who grow extra muscle when the gene itself should code for not growing muscle.
Insertion: when a sequence is added to a gene, like when a mutated extra sequence causes peas to grow with less starch and sugar and become wrinkled instead of smooth.
Gene Copy Number: extra copies of genes are created and passed on, like the starch gene was made 10 times in humans but only once in chimps.
Duplication: when the same base pair appears more than 8 times in a row it is very likely to be copied incorrectly during cell reproduction. Homopolymers like the C-G pair in pigs cause light colored vs spotted coats when copied incorrectly.
Regulation error: when the part of the gene that codes for when each part of the sequence kicks in is copied incorrectly, examples include the teosinte plant versus the modern day corn plant.

4. What is evo-devo? 
The specialized study of the way genes and mutations affects evolution.

5. Make a connection between human migration and the mutation of lactose intolerance.
Lactose intolerance is default for populations who only feed milk to their babies, not their adults. the mutation of lactose tolerance developed when humans migrated with their hunting sources but settled down to become agricultural societies in China, Europe, and the Middle East and needed to digest milk products from their domesticated prey.  

Human History is Written in Genes

Though we consider our species incredibly advanced, 99% of our gene sequence is identical to the gene sequence of chimpanzees. And though we consider our species incredibly diverse, even going as far as to attack fellows of our species on account of their phenotypes, we are genetically even less different from other human beings than from chimpanzees- less than 1% to be precise. In context of the scientific, genetic explanation for human diversity, our previous hypotheses about our origin and the distinction between races seem outdated.

            For one thing, it’s highly likely that all the humans on earth are descended from a single mother, a “mitochondrial eve”(Shreeve, 62)*. We know this because mitochondrial DNA is passed down directly from mother to child with all the previous mutations preserved, and the earliest and most ubiquitous mutation originated in Africa. Scientists deduce that a group of people in Africa decided to migrate out because the genetic markers of those people still appear all around the world. This means that everyone alive today is descended from those people who lived in Africa. Scientists have isolated the most common and thus the earliest genetic markers, and the San bush people of southern Africa, the Biaka Pygmies of central Africa, and tribes in eastern Africa seem to be the source of those genetic markers. Scientist Spencer Wells met with the San people, and they exhibit various phenotypes present in other groups of people. The scientific explanation for the population of the earth- that humans are the ones who did the traveling and the creating, not creator gods- chafes with traditional origin stories. For example, Wells received a flat-out denial of his research from an Aboriginal man who chose to support the origin stories of his own culture. Nevertheless, evidence indicates all humans are distant relatives from Africa.

             Race as defined by skin color is also a social construct that genetics refutes. Skin color varies from light to dark as an adaptation to millennia of sun exposure, and doesn’t exclusively indicate genetic similarity. People from Africa may have the same skin tone as Aboriginal Australians, and still be genetically distinct in almost every other way. It is true that different evolutionary populations have common polymorphisms- Alus and short tandem repeats are two types of gene sequences that are inheritable. Scientists can group people based on the amount of common Alus or short tandem repeats they have, but with varying degrees of accuracy. There is debate over whether it’s even useful to group populations based on gene sequences that don’t inherently code for anything vital to survival. But there is research that indicates some populations have adaptive traits from long ago that are medically relevant to disease treatment and prevention today. If people can be categorized into their genetic groupings, doctors can better search for genetic traits that may influence their diagnoses and treatments. Despite the potential benefits of grouping people genetically, it is still too close to the practice of racial profiling for many scientists’ comforts.  

            Gene sequencing supports the theory of evolution by demonstrating the similarities between humans and other primates. It also shows the process of random mutation and natural selection over time. The human population is one of the best sources of raw data on evolution. We have populations with very little immigration, we have populations who have emigrated to other climates, we have populations who have mixed in one region, and we have populations who have mixed in many locales. Though genetic sequencing hits some controversial nerves on origin and race, disrupting social constructs may be exactly what we need to progress as a species.  

*Shreeve, James. "The Greatest Journey Ever Told." National Geographic. March 2006. pages 62-69.

Hardy-Weinberg

Evolution will not occur if
1. the sample size is large and thus everything is more evenly random
2. mating is random- there is no particularly attractive trait
3. DNA does not mutate
4. There is no differential migration, where new genes are introduced
5. phenotypes do not influence survival

p*p + 2pq + q*q = 1
p+q=1
these equations detail the rates of occurrence of alleles and genotypes.
dominant alleles are p and recessive alleles are q.

If the entire population is allowed to breed randomly, then an equilibrium will remain in the sample. 0.5 vs 0.5 dominant and recessive alleles. But if the population is separated, the final occurrence of dominant and recessive alleles will not be 0.5 vs 0.5.

Natural Selection

Genotype- the gene sequence that an organism inherits from its parents.
Phenotype- the characteristics an organism shows as a result of their genes.

There is a dominant and a recessive allele. The dominant allele will determine the phenotype whenever it appears. The recessive allele will show if it is the only allele in the genotype.

In the case of Bengal Tigers, a recessive phenotype means no fur. And no fur means death in the winters. So we did an experiment on natural selection's effects on a gene pool. We used colored beads to represent alleles, and picked them two at a time randomly out of a bag.
Each time we got a recessive phenotype, those bead alleles were eliminated. Eventually after about 6 generations of random breeding, the recessive phenotype stopped occurring, thought the recessive alleles remained in the gene pool.

Natural selection is the process of eliminating those traits that do not help survival. Evolution operates on populations over time, not individuals. Individuals just die and fail to pass on their genes.

Brine Shrimp

We hatched Brine Shrimp!
Brine Shrimp have evolved a mechanism that allows them to stay in egg stage until the time is right to hatch. Their criteria involve a particular solution of salt- no more, no less.
We placed varying concentrations of salt water (% by mass) into petri dishes, then placed glass slides covered with around 20 brine shrimp into solution. We waited 24 hours, took stock of how many shrimp were swimming, then took a second set of measurements at 48 hours.
Our class data was off because we committed some human errors.
We may have miscounted the shrimp.
or
mixed up the saline solution labels.

Our class graph indicated the optimum salinity for brine shrimp to be 0.5% NaCl.

Fava Beans

Fava beans are known commonly as broad beans. 

They look every inch a healthy food, and would be except that for many people they are actually toxic. If your ancestors hailed from a region suspect to malaria back in the day, you would inherit a trait that made you lack enzyme G6 PD. Favism would cause an allergic reaction in your body, the symptoms of which include diarrhea, hemolytic anemia (breakdown of your blood cells), and thus extreme fatigue.This affects mostly people from the Mediterranean and Africa. This evolved as a way of preventing the carrier of the G6 PD deficiency from Malaria, because the disease could not infect those with Favism.