Category: Big Idea 1

Weekly Reflection #6

On By patrickledouxbiologyIn Big Idea 1

Tundra_Biome_600

This week we began learning some biochemistry, focusing on the properties of water. To start, we reviewed and defined the three subatomic parrticles we will need to know:

  • protons: positively charged particles found in the atom’s nucleus. Have a mass of 1 amu and a charge of +1
  • neutrons: neutrally charged nucleus particles, mass of 1 amu
  • electrons: negatively charged particles that orbit the nucleus. Basically massless and have a charge or -1

These are all what makes up an atom. An element is a type of atom with a specific number of protons, and is the smallest unit of a substance that still retains its properties. (ex. carbon, 6 protons). There are about 120 different elements represented on the periodic table, of which biology uses CHONPS (carbon, hydrogen, oxygen, nitrogen, phosphorous, silicon) most of the time.

We also learned about how atoms interact, i.e. different types of atomic bonds.

  • Bio Covalent
  • Covalent Bonds- bonds created by atoms ‘sharing’ an electron. Ex. O=O bonds or C-H bonds. These bonds are relatively strong.
  • Ionic bonds- created when one atom gives an electron to another atom. This usually happens to complete the outer shell(s) of one or both atoms. This creates an attraction between the atoms as one atom is now negatively charged while the other is positive. In general these bonds are relatively strong.
  • Hydrogen Bonds- Intermolecular bonds that form between the positively charged hydrogen of a polar molecule and the partially negatively charged oxygen or nitrogen end of another polar molecule (ex. H — O bonds between water molecules)

Next, we learned about why water is so important to human bodies. The primary reason for this is that water has a high specific heat (4.184 J/g*C). This means that it takes a lot of energy to change the temperature of an organism containing lots of water, so it is easier for said organism to maintain homeostasis.

Next we had a discussion of the pH scale and what it measures.  We read an interesting set of stories that explained how a lower pH (0-7) indicates an acidic solution, while a high pH (7-14) indicates a basic solution. An acid is a substance that donates protons to solution, like HCl, while a base is a substance that accepts protons (like bleach). The pH of a solution is the -log[H+].

Questions Going Forward

Will we need to memorize the body’s buffer compounds? How much chemistry will we need to know for the AP test? Will we do a lab regarding pH or specific heat?

 

Weekly Reflection #4 – HWE

On By patrickledouxbiologyIn Big Idea 1

This week’s focus was all Hardy-Weinberg Equilibrium.

Image result for hardy-weinberg equilibrium

We learned the history behind the HWEQ equation, who discovered it, and how to properly use it. We also focused on the conditions necessary for HWEQ. We started out with defining some terms as they relate to Hardy-Weinberg:

  • Gene-  DNA that determines a trait
  • Allele – A variant of a trait (DNA)
  • Dominant Allele – Shows a trait/phenotype, regardless of the other allele.
  • Recessive Allele – An allele that only shows when paired with another recessive.
  • Homozygous – A matching allele pair (PP, dd, hh, KK, etc.)
  • Heterozygous – An unmatched allele pair (Pp, Dd, Hh, Kk, etc.)
  • Evolution – Change in allele frequencies over time.
  • Population – a localized group of interbreeding individuals.
  • Gene Pool – The collection of all the alleles present in a population.
  • Mutation – Creates variation/ new and novel traits. Always happening.
  • Gene Flow – Movement of organisms into/out of a population, changes allele frequencies.
  • Non-Random Mating – Causes sexual selection and sexual dimorphism.
  • Genetic Drift – Random, chance events that change the gene pool.

After learning these terms, we went over the conditions necessary for a population to in HWE, listed below.

  1. Random Mating
  2. No Mutations
  3. No Gene Flow
  4. No Natural Selection
  5. No Genetic Drift

As you can see, very few real-world populations are actually in HWE. What is the purpose of HWE then, if it fails to describe reality? This was an important question this week. Turns out HWE is best used as a null model- a control group.  If you calculate the allele frequencies for a population if it stopped evolving and changing altogether, you can then see how that population has evolved over time compared to the null model. We did a lab to try this technique out on Friday to see if we could achieve HWEQ amongst ourselves. No surprises, we couldnt.

HWE Equation: p^2 + 2pq + Q^2 = 1,     p + q = 1

Synthesis/Questions Going Forward

HWE seems to pull together everything we’ve been learning the past few weeks. It brings all the vocab and methods of evolution and types of alleles into play. This feels like the first relatively powerful tool we’ve received, akin to M1V1 = M2V2 in Chemistry. But how will we better mathematically describe populations and allele frequencies in the future? How will we better simulate reality? Are there ways to account for the things HWE must hold constant?

Big Idea #1

Image result for six fingered amish

 ^ Polydactyly ^

 

 

 

Weekly Reflection #3

On By patrickledouxbiologyIn Big Idea 1

9/23 – 9/28

This week we covered many topics related to evidence for evolution. We began by defining several terms, as to avoid confusion with the way they are used in common speaking.

  • Falsifiability: the idea that scientific thoughts can never be 100% proven, only supported by evidence.
  • Hypothesis: A testable Statement
  • Theory: A major unifying framework supported by all evidence currently known.
  • Law: A deduced fact that will always hold true.

We then discussed the names for the various structures used in comparative anatomy that suggest evolution. Comparative anatomy is a method of deducing organism’s evolutionary relationships by comparing similar structures in their bodies.Image result for comparative anatomy structures

  • Homologous Structures: similar structures in related organisms that serve independent purposes. These suggest that organisms share a common ancestor that had this structure.

 

  • Image result for comparative anatomy structures Structures: Similar adaptations to similar situations and problems (these serve as evidence for convergent evolution)
  • Vestigial Structures: Structures that no longer serve any or very little function, but don’t cause the organism to be selected against (Like the human appendix or the pelvic bones and femurs of whales).

Another topic we covered was the development of phylogenetic (or evolutionary) trees. We learned how modern DNA sequencing results have helped scientists build more expansive and accurate trees, as comparing DNA sequences can reveal evolutionary histories often better than comparative anatomy.Image result for phylogenetic tree

Ongoing Questions:

How is DNA actually collected and read? Can we recreate synthetic DNA? If so, could we design our own synthetic organism? Would that organism be in its own synthetic domain?

HHMI Activity Link: https://www.hhmi.org/biointeractive/creating-phylogenetic-trees-dna-sequences

 

Sept 10-14 Weekly Reflection

On By patrickledouxbiologyIn Big Idea 1

What we learned this week

This week we learned the difference between and how to calculate standard deviation and standard error. I struggled a bit at first to really understand what these two numbers meant in the context of a data set, but made sure I at least somewhat knew what they were before Friday’s quiz. We then discussed the five pathways of evolution, and looked at examples of evolution in galapagos finches and desert pocket rock mice. We watched clips of a documentary and completed worksheets for each. Finally, we took notes on how the theory of evolution was developed and who contributed to it. Most of the scientists and ideas sounded familiar from freshman-year biology, but a refresher never hurt anyone. Most of these notes and the topics covered this week related to Big Idea #1.

Five Types of Evolution

These categories are how we learned to classify types of evolution, or a change in a population over time. I thought it was interesting that evolution could be influenced in so many unique ways, not limited to natural selection and mutations.

  • Natural Selection
    • The process by which those organisms with traits best fit to the environment survive and reproduce more than those with less suitable traits. This causes a change in the population over time that favors the fitter traits.
  • Mutation
    • Errors that occur while reproducing genetic material. Mutations can either be positive, negative, or most commonly, neutral. The most visible kind of mutation are positives, as neutral mutations do not usually have any effect and organisms with negative mutations wont be able to compete as well and will die out. Positive mutations will cause a change in a population as their organisms will have a competitive advantage over their brethren.
  • Preferential Mating
    • Change in a population caused by organisms preferring to choose mates with certain favorable traits.
  • Migration/Gene Flow
    • When populations of organisms move from one area to another, this causes change in the  makeup of the populations of both the old and new areas. If there is a population of 50 geese with red feathers on a lake, and 25 more geese with blue feathers are forced to move to the lake, the population of the lake has changed from 100% red to 2/3 red, 1/3 blue.
  • Genetic Drift
    • Chance changes to a population. If all the blue geese from above happen to be struck by meteors, the population makeup has changed, but only by chance.

Beaks of Finches, Shades of Mice

Image result for galapagos finches

The primary examples of evolution we focused on this week were in galapagos finches and rock pocket mice populations. For the finches, we observed how different beak sizes in differing situations performed better or worse, like in the drought of 1976. The effects of the drought caused large seeds, the food of big-beaked-birds, to become scarce. This forced the BBB’s to eat smaller seeds, which their large beaks were not very good at. Here we can see that the birds with smaller beaks have become more competitive as the environment changed, and the surviving proportion of birds with smaller beaks was accordingly larger than before the drought. In the documentary we were introduced to the scientists who had dedicated much of their life’s work to catching, tagging and tracking hundreds of finches in order to observe this. This was a good example of evolution caused by natural selection.Image result for rock pocket mice

We were presented with a similar story in the case of the rocket pocket mice. These mice lived in the deserts of Arizona, and were well camouflaged to blend in to the light-colored ground. This changed when a few thousand years ago volcanic eruptions took place nearby, spreading great lava flows out over the desert which cooled into slabs of black rock. The brown-colored mice now stood out in high contrast with the black earth, and so were easy picked off by predators like hawks and owls. The mice did not go extinct on the lava flows, however, as a few were born with a mutation that would have been a disadvantage back in the desert. This mutation effected the gene that controlled the mouse’s production of melanin, the protein that causes the dark color in mammal fur and skin. The mutated mice were dark in color, blending in to the dark lava flows. Sure enough, after several generations nearly all mice living on the flows were black. This was another simple example of natural selection, but also displayed how beneficial mutations can quickly change a population.