Introduction

Question 1

Phylogenetics

Answer 1

Evolutionary process over millions of years

Question 2

Population Genetics

Answer 2

Evolution within a species focusing on the genetic variation among people

Question 3

Evolution will be treated as a mathematical process (in this class)

Answer 3

mathematical process

Question 4

Biological evolutionary processes operate on several scales

Answer 4

cellular (in the body) / somatic

Tens/hundreds of thousands of years

Millions of years

Question 5

Addressing most read world problems in data science requires using a mix of toolkits

Answer 5

tools like matlab, Python

Question 6

Central Dogma in Biology

Answer 6

DNA - RNA - Protein

These are the major classes of polymers

Proteins are not used to go back to creating DNA or RNA.

RNA reverses transcribes to DNA in special cases

Question 7

Genetic sequence is ideal natural representation

Answer 7

Linking biology and data

Question 8

DNA is represented by “alphabet”

Answer 8

A , C , G ,T

Question 9

RNA is represented by “alphabet”

Answer 9

A, C , G , U

Question 10

Proteins have an alphabet of 20 letters (sometimes more) representing Amino Acids that make up proteins

Answer 10

Proteins

Question 11

Transcription

Answer 11

DNA to RNA (1 to 1 mapping)

Most of the DNA in most genomes (e.g., 75% in humans and 15% in bacteria)
are not part of “genes”. These regions are not transcribed.

Question 12

Translation

Answer 12

Protein are synthesized using the informatio in m(RNA). Protein are the building blocks of living cells

Different cells “express” RNA/Protein of each gene
at various levels and in multiple forms (splicing)

Question 13

How does the 4 letter DNA/RNA code for 20 letter (Amino Acid) proteins?

Answer 13

Three DNA/RNA letters ion arow, called codon, code for one amino acid

There are 4^3 = 64 codons, but only 20 amino acids. There is redundancy

Question 14

LEss than 2% of genome is for coding

Answer 14

Exons: protein coding regions

Stop codons: gene boundaries

Introns: regions between exons. Introns are transcribes but not translated

Question 15

DNA Replication / Mutation

Answer 15

Parts of the molecule occasionally change in the new copy. These events are called mutations

Question 16

DNA Replication / Substitution

Answer 16

Most common form of mutation where one letter changes to another letter

Transition: substitution between A and G or between C and T

Transversion: other cases

Transitions are more liely than tranversions. This has to do with the chemistry of DNA, plus properties of the reduntant genetic code

Question 17

Indels

Answer 17

insertions or deletions (common)

Question 18

Complex types like inversion, gene duplication, gene transfer, segmental duplication, rearragnement, etc.

Answer 18

.complex types of changes

Question 19

Sequence Evolution

Answer 19

Just as various organisms look similar they also have similar genetic material.

For example chimps and humans are 95% similar

Question 20

Each mutation starts with one individual from a “species”

Answer 20

Through time, mutations may survive to future generations and may eventually get “fixated” so that all/most individuals in that population include the mutation

Reason for fixation is natural selection. Another mechanism is genetic drift: random chance leading to fixation of changes. Others include sexual selection

Question 21

Time + many of mutations can eventually generate a new organism

Answer 21

Sequence evolution

Question 22

Evolutionary Trees show relationships through evolutionary time

Answer 22

Phylogeny

Question 23

Tree topology (branching structure of the tree)

Answer 23

Nodes can represent species, viruses, different genes in the genome of one or several species, or even languages

Internal nodes typically correspond to extinct species/genes/etc. Leaves correspond to extant species/etc.

Edge indicates the parent node evolved to the child node. Leaves below an internal node are its evolutionary decsendants

Question 24

Branch Length

Answer 24

shows some notion of time or amount of change between nodes

Question 25

How do we study biological data

Answer 25

Define clean optimization problems. Ex. Align sequences by optimizing similarity between matched positions

Build mathematical models. A generative model can create a sequence data “just like” what we see in reality. Typically statistical models

Question 26

How do we build models

Answer 26

Seek to capture mechanisms behind actual processes that generated the data

Or forget the data, but build descriptive models that seek to emulate patterns seen in the data, regardless of mechanism.

Where do we get data and their patterns. REquires a reference data set to train from. This is associated with machine learning

Question 27

Models are always wrong, but some are useful (George Box)

Answer 27

Whether mechanistic or not, models are simplfying representations of reality

See Geman and Geman 2016 SCIENCE, for debate between camps