Running_List_of_Goals_Slides_Assignments_2024

Lecture 11

Goals

Assignment for Wednesday (11/5)

Play with Paul Lewis's MCRobot. Explore a differing number of heated chains, and different probability landscapes. https://plewis.github.io/applets/mcmc-robot/
Work through Olga's webpage giving an example on Baysian thinging


Computer lab 10

Computer-lab assignment 10; pdf

Goals

Assignments for Monday see below.


Lecture17

Goals

Assignment for Friday

Assignment for Monday (10/30)


Lecture16

Goals

Assignment for Wednesday


Computer lab 9

Computer-lab assignment 09; pdf

Goals

Assignment for Monday


Lecture 15

Goals

SLIDES on lab 8, Gene and Genome Duplications, Mutual aid

Assignments for Friday


Computer lab 8

Computer-lab assignment 08; pdf

Goals


Lecture 14

Goals

slides on Images to depict evolution, Mutualism and Mutual Aid

Assignments for Monday


Lecture 13

Goals

Slides on lab 7, photosynthesis in the ToL and cladistics.

The heat of this controversy is reflected in the following excerpt from from Tom Cavalier Smith http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842702/ :
"Oddly, the school of ‘phylogenetic systematics’ founded by Hennig (1966) grossly downplayed the phylogenetic importance of progressive change compared with splitting, seen by them as so all-important that many Hennigian devotees dogmatically insist that ancestral groups like Bacteria, Protozoa and Reptilia be banned. Hennig called such basal groups with a monophyletic origin ‘paraphyletic’ and redefined monophyly to exclude them and embrace only clades, likewise redefined as including all descendants of their last common ancestor. This redefinition of ‘clade’ is universally accepted, but Hennig's extremely confusing and unwise redefinition of monophyly is not. Though accepted by many, sadly probably the majority (especially the most vociferous and over self-confident, and those fearful of bullying anonymous referees, of whom I have encountered dozens mistakenly insisting without reasoned arguments that paraphyletic taxa are never permissible), it is rightly firmly rejected by evolutionary systematists who consider the classical distinction between polyphyly and paraphyly much more important than distinguishing two forms of monophyly (paraphyly and holophyly, using the precise terminology of Ashlock (1971), where holophyletic equals monophyletic sensu Hennig)."


Computer lab 6

Computer-lab assignment 07 docx
Computer-lab assignment 07 pdf

Goals

Assignment for Monday

Read through the letter of Ernst Mayr criticizing Carl Woese's three domain classification. Woese's reply is here but it is rather lengthy. Instead, read the shorter argument to abolish the term prokaryotes by Norm Pace here.


Midterm

In TLS 301, bring a pencil and eraser.


Lecture 12 (10/7)

Goals

Slides gene drive in phage populations, inferring within genome recombination events from gene and nucmer plots

Assignment

for Friday (10/11)

Make sure that you know where you saved the sequences you retrieved and analyzed in lab 4 (the phage intein and extein sequences) and lab 6 (the genome sequences of selected bacteria)


Computer lab 6

Computer-lab assignment 06 docx
Computer-lab assignment 06 pdf

Goals

Assignment

for Monday

Think about questions to ask before the midterm.


Lecture 11 (10/2)

Goals

Slides on arguments against a hyperthermophylic LUCA, Strand Bias, Recombination and AIMS

Assignments

for Friday (10/4)

for Monday (10/7)


Lecture 10, 9/30

Goals

Assignments for Wednesday 10/2


Computer lab 5

Computer-lab assignment 05 docx
Computer-lab assignment 05 pdf

Goals

Assignment for Monday

read as much of this [introduction to the unix shell]


Lecture 9 (9/25)

Goals

Assignments for Friday 10/1


Lecture 8

Goals:

Assignments for Wednesday 9/25


Computer lab 4

Computer-lab assignment 04, pdf

Goals


Lecture 7 (9/18)

Goals

Assignments

for Friday's (9/20) Computer Lab

for Monday's Class 8 (9/23)


Lecture 6 (9/16)

Goals

Assignments for Wednesday class 7 (9/20)


Computer lab 3 (9/13)

Assignment 03.docx , pdf:
Characterizing homing endonuclease and self-splicing domains in inteins using chimeraX / using alphafold to predict protein structures.


Lecture 5 (9/11)

Goals

Assignments

for Friday (9/15)

for Monday (9/16)

  1. Draw a sketch for the relation between the number substitutions that occurred in evolution and the percent identity of the two sequences. (I.e. how does the observed similarity change, as more and more substitutions occur?)
  2. What are the endpoints (saturation levels) for 4 letter alphabet and for a 20 letter alphabet assuming a perfect alignment that aligns homologous positions.
  3. How does this relationship change, if some parts of the sequence are so important that the protein becomes non-functional, if a mutation occurs in these positions (i.e., these parts of the sequence are never observed to undergo any change?
  4. If you were to do a realistic calculation and you were to consider a nucleotide sequence, how long would it take to arrive at less than 25% identity? (tip: how similar are two random sequences that have not been aligned?)
    (Note: answering these questions should not require the use of a calculator or a formula, just common sense.)

Lecture 4 (9/9)

Goals

Note For those who joined the course recently

Look through the slides linked below, and if they do not make sense, check the recordings on HukyCT. Ask the instructors in some things remain unclear.

Assignments:


Computer lab 2 (9/8)

Assignment 02.docx , pdf:
Aligning divergent sequences and structures in Chimera

Goals:

Assignments for Monday:
Read through the Slides on the ATP synthase (skip the intein slides), and try to understand how the evolution of ATP subunits (and other ancient duplicated genes) informs us on the early evolution of life.


Lecture 3 (9/4)

Goals:


Assignments for Friday


Computer Lab #1 (9/1)

Computer-lab assignment 01 docx; pdf
Intro to Chimera: Binding Pocket - Substrate Interactions


Goals:


Assignments for Wednesday see below



Lecture 2 (8/30)

Goals:

Assignments for Friday (8/30):

Assignments for Wednesday (9/4)

Contemplate the following questions (see the slides on homology for inspiration):

Try to answer the following questions:

Read the excerpt from Thomas Mann's book on Dr. Faustus (Dr Faustus) available on HuskyCT. Or at https://www.fadedpage.com/showbook.php?pid=20180329 (go to chapter III). This chapter can provide two insights:

Ask a question (not limited to Dr. Faustus) on the huskyCT discussion board


Lecture 1 (8/26)

Goals:

Assignments for Wednesday (8/30):

Assignments for Friday (8/30)