BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 7.
Introduction to Microbial Diversity.
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human ...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 11.
Symbioses and the Human MIcrobiome
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 8.
Introduction to Microbial Diversity, part 2.
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 7.
Introduction to Microbial Diversity.
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human ...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 11.
Symbioses and the Human MIcrobiome
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 8.
Introduction to Microbial Diversity, part 2.
Slides for Lectures by Jonathan Eisen
Bio chapter 1 biochemistry, the cell, & geneticsAngel Vega
Evolution, the Themes of Biology, and Scientific Inquiry

KEY CONCEPTS
1.1 The study of life reveals common themes
1.2 The Core Theme: Evolution accounts for the unity and
diversity of life
1.3 In studying nature, scientists make observations and form and test hypotheses
1.4 Science benefits from a cooperative approach and
diverse viewpoints
Similar to BIS2C_2020. Lecture 6. The Tree of Life. (20)
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Thoughts on UC Davis' COVID Current ActionsJonathan Eisen
Slides I used for a presentation to Chancellor May's leadership council about the current state of UC Davis' response to COVID and how it could be improved
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
3. 1.Give examples of universal traits shared by all
organisms
2.Understand how to determine which of these are
evidence for common ancestry of life
3.Understand what “universal homologies” are
4.Understand why the existence of universal
homologies means all life on earth has a
common origin
5.Understand how to determine if life on another
planet has common origin to life on Earth
Lecture 6 Learning Goals
4. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
5. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
7. Background: About Me
• Jonathan Eisen
• At UC Davis since 2005
• Evolution & Ecology
• Medical Microbiology and
Immunology
• Genome Center
• Center for Population Biology
• Web site: phylogenomics.me
• Tree of Life Blog:
phylogenomics.blogspot.com
• Twitter: @phylogenomics
• Ted: tinyurl.com/EisenTed
8. • Lab 1: Introduction to Phylogeny
!Phylogenetic methods
!Phylogenetic trees
!Homology, homoplasy
!Characters, character states
Background: Lab Connections
9. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
10. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
13. Tree of Life vs. Trees of Life
“As buds give rise by growth
to fresh buds, and these, if
vigorous, branch out and
overtop on all sides many a
feebler branch, so by
generation I believe it has
been with the great Tree of
Life, which fills with its dead
and broken branches the
crust of the earth, and covers
the surface with its ever-
branching and beautiful
ramifications.”
Darwin, 1872
14. “There is grandeur in this
view of life, with its several
powers, having been
originally breathed into a
few forms or into one; and
that, whilst this planet has
gone cycling on according
to the fixed law of gravity,
from so simple a beginning
endless forms most
beautiful and wonderful
have been, and are being,
evolved.”
Tree of Life vs. Trees of Life
15. Key Questions for Today:
• Is there a single tree of life or are there
multiple trees of life?
• Is there a single origin for all of life, or
are there multiple origins?
Tree of Life vs. Trees of Life
16. Tree of Life vs. Trees of Life
Connect
These on a
Single Tree
of Life
29. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
30. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
31. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
33. Which of the following is NOT a universal
trait of all of life?
A: Made up of cells
B: Carry out transcription and translation
C: Extract energy from the environment
D: Universal molecular code to make
proteins
E: Contain genomes inside a nucleus
Thought Question
34. Which of the following is NOT a universal
trait of all of life?
A: Made up of cells
B: Carry out transcription and translation
C: Extract energy from the environment
D: Universal molecular code to make
proteins
E: Contain genomes inside a nucleus
Thought Question
35. The basic structural and physiological
unit of most living organisms is the
A: Organelle
B: Aggregate
C: Genome
D: Cell
E: Membrane
Thought Question
36. The basic structural and physiological
unit of most living organisms is the
A: Organelle
B: Aggregate
C: Genome
D: Cell
E: Membrane
Thought Question
39. List traits found in all organisms.
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Existence of
universal traits
does not prove all
life has a common
origin
Universal Traits
40. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
• Martians
41. Homology
Similarity that is due to inheritance from a
common ancestor
Homoplasy
Similarity that has evolved independently
Homology vs. Homoplasy
44. List traits found in all organisms.
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Universal Traits
Yes: not evidence
for common
ancestry.
No: evidence for
common ancestry.
Could trait have
evolved with a
reasonable
probability in
separate origins of
life?
46. Uses Water as Solvent
Homology vs. Homoplasy: Water
Could “uses water as a solvent" have evolved with a
reasonable probability in separate origins of life?
47. Uses Water as Solvent
Homology vs. Homoplasy: Water
If YES: “uses water as a solvent" could have evolved with a
reasonable probability in separate origins of life
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
48. Uses Water as Solvent
Homology vs. Homoplasy: Water
If NO: “uses water as a solvent" could not have evolved with a
reasonable probability in separate origins of life.
Then only possibility is a single tree.
49. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Water abundant and likely only major
available solvent for life.
50. Uses Water as Solvent
Homology vs. Homoplasy: Water
YES: “uses water as a solvent" could have evolved with a
reasonable probability in separate origins of life.
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
52. Homology vs. Homoplasy: Cells
Cells: Membrane bound compartments that are the
fundamental building blocks of all organisms
53. Uses Cells
Homology vs. Homoplasy: Cells
Could “uses cells” have evolved with a reasonable
probability in separate origins of life?
54. Homology vs. Homoplasy: Cells
If YES: “uses cells" could have evolved with a reasonable
probability in separate origins of life
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
Uses Cells
55. Homology vs. Homoplasy: Cells
If NO: “uses cells” could not have evolved with a reasonable
probability in separate origins of life.
Then only possibility is a single tree.
Uses Cells
56. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Cell-like structures can
form from very simple
components under early
life conditions
57. Homology vs. Homoplasy: Cells
YES: “uses cells” could have evolved with a reasonable
probability in separate origins of life.
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
Uses Cells
58. Uses DNA as Genetic Material
Homology vs. Homoplasy: DNA
59. Homology vs. Homoplasy: DNA
Nucleic acids are made up of
chains of nucleotides.
Nucleotides are made up of a
sugar, a base, and and a
phosphate
DNA = deoxyribonucleic acid
RNA = ribonucleic acid
60. Uses DNA as Genetic Material
Homology vs. Homoplasy: DNA
Could “uses DNA” have evolved with a reasonable
probability in separate origins of life?
61. Homology vs. Homoplasy: DNA
If YES: “uses DNA” could have evolved with a reasonable
probability in separate origins of life
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
Uses DNA as Genetic Material
62. Homology vs. Homoplasy: DNA
If NO: “uses DNA” could not have evolved with a reasonable
probability in separate origins of life.
Then only possibility is a single tree.
Uses DNA as Genetic Material
63. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Nucleotides form in early Earth
conditions. DNA might form too and thus
could readily be used by different origins
of life.
64. Homology vs. Homoplasy: DNA
MAYBE: “uses DNA” could have evolved with a reasonable
probability in separate origins of life.
Thus it is unclear if this trait requires a single tree of life or if
multiple trees are possible.
Uses DNA as Genetic Material
65. Homology vs. Homoplasy: DNA
Might be evidence that there is one tree.
Uses DNA as Genetic Material
69. Could “the central dogma” have evolved with a reasonable
probability in separate origins of life?
Central Dogma
Homology vs. Homoplasy: Central Dogma
CD CD CD CD CD
70. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
No clear reason why or how a separate
origin of life could or would end up with
DNA»RNA»protein
71. Central Dogma
CD CD CD CD CD
CD
CD
CD
CD
Homology vs. Homoplasy: Central Dogma
NO: “uses central dogma” likely could not have evolved with a
reasonable probability in separate origins of life.
Then only likely possibility is a single tree.
72. Thus multiple origins of life is not likely
Central Dogma
Homology vs. Homoplasy: Central Dogma
CD CD CD CD CD
CD
CD
CD
76. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Absolutely no way a separate origin of
life would use the same ribosomes,
with 50+ proteins, multiple rRNAs, and
similar 3D structures and mechanisms
77. NO WAY: “uses ribosome for translation” could have evolved in
separate origins of life.
Then only possibility is a single tree.
Homology vs. Homoplasy: Ribosome for Translation
Ribosome For Translation
79. List common traits of all organisms.
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy
80. Easily could be
homoplasious
List common traits of all organisms.
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy
81. Might be
homoplasious
List common traits of all organisms.
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy
82. Likely
Homologous
List common traits of all organisms.
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy
83. List common traits of all organisms.
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Definitely
Homologous
Homology vs. Homoplasy
84. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
• Martians
86. Universal Homology
Trait shared by all organisms that could not
have arisen in separate origins of life and
thus is evidence for common ancestry.
Universal Homology
88. Hypothesis 2:
Common Origin
Hypothesis 1:
Separate Origins
Two Hypotheses
Tree of Life vs. Trees of Life
The existence of Universal
Homologies means all life on
Earth is related.
89. “There is grandeur in this
view of life, with its several
powers, having been
originally breathed into a
few forms or into one; and
that, whilst this planet has
gone cycling on according
to the fixed law of gravity,
from so simple a beginning
endless forms most
beautiful and wonderful
have been, and are being,
evolved.”
Tree of Life vs. Trees of Life
90. “There is grandeur in this
view of life, with its several
powers, having been
originally breathed into a
few forms or into one; and
that, whilst this planet has
gone cycling on according
to the fixed law of gravity,
from so simple a beginning
endless forms most
beautiful and wonderful
have been, and are being,
evolved.”
Tree of Life vs. Trees of Life