Biology 1010 Lecture Notes

Unit 1. Origin and Early Evolution of Life on Earth

These notes were last updated September 10, 2001

Some key words, phrases, and ideas :

• science vs pseudoscience vs not science
• natural forces vs supernatural forces
• species--definitions and Latin bionomials
• Lamarckian evolution vs Darwinian evolution
• Oparin-Haldane model; Urey-Miller experiment
• RNA/protein-based metabolism
• Eubacteria vs Archaea vs proto-Eucarya
• chemoheterotrophy vs chemoautotrophy vs photoautotrophy
• fermentation vs anaerobic respiration vs aerobic respiration; membrane-bound electron transport chains
• anoxygenic photosynthesis vs oxygenic photosynthesis

1. Introduction
1. basic questions for the course
1. What is a species?
2. How many species are there?
3. Where did they all come from?
4. How do they interact with each other and with the environment?
2. early approaches
1. Plato and Aristotle--ideals, the scalae naturae, and special creation
2. Linnaeus--Latin binomials, heirarchy based on structural relationships
1. New questions:  What do these relationships mean? What are fossils and what does the fossil record mean
3. de Buffon--centers of creation; still not scientific and does not explain fossil
3. scientific approaches
1. What is science? How is the scientific approach different from other approaches?
2. Hutton and Lyell and the age of the Earth
3. Lamarck and the theory of evolution by acquired characteristics
1. based on the changes seen in the fossil record of a certain group of snails
2. basic mechanism:
1. individuals develop needed traits, lose unnecessary or unused traits
2. changes made in parents are passed along to offspring
3. rejected at first because the idea of evolution was not accepted, later because no known force to account for the development of needed structures in a way that can be inherited by offspring (note: many educated people believe in Lamarckism without realizing it)
4. Darwin used his own observations of relatedness, plus Hutton's and Lyell's interpretation of the geologic record, plus Malthus's ideas concerning the growth of populations to develop a theory of evolution by means of natural selection
1. basic mechanism
1. more offspring are born than will reached maturity--losses caused either by limited resources or by predation (superfecundity and the struggle for existence)
2. while on average offspring are the same as their parents, there is a great deal of genetic variability within a family or species (individual variation and heredity)
3. some of that genetic variability gives organisms a better chance to reproduce (better competitors or better at avoiding predators or something along those lines)
4. a greater proportion of the next generation is born of parents with the "good' variation, with a better chance at surviving and reproducing so that adaptive traits tend to accumulate within a population
2. tests of the theory
1. the fossil record supports the idea of evolutionary change
2. comparative anatomy (homologous structures) indicates relationships among existing organisms
3. comparative embryology indicates relationships among organisms
4. comparative mlecular biology indicates relationships among organisms
5. Haldane and others provided the means to test evolution on the microscale
5. new problem:  What is the source of genetic variation?
1. initially much confusion between genetic and acquired variability and about how the variability is passed on
2. Mendel's work with pea plants helped, but was ahead of its time; needed evidence from microscopy to support his views
3. Griffith discovered that traits could be passed from bacterium to bacterium (even if dead), implying that traits are carried by particular chemicals; Avery demonstrated that the chemical involved was DNA; Watson and Crick showed how DNA could work as genetic material; we are now able to manipulate DNA to create new variants
2. Earth's earliest biosphere
1. sources of information
1. structure of the solar system, composition of meteorites
2. geologic history of Earth (times based on layering in sedimentary rocks and radioisotope dating of the rock material)
1. Hadean (4,500 mya to 3,800 mya) -- formation of the Earth, solidification of the crust
2. Archean (3,800 mya to 2,400 mya) -- beginnings of life on Earth
3. Proterozoic (2,400 mya to 550 mya) -- rise of oxygen in the atmosphere, advanced unicellular life on Earth
4. Paleozoic (550 mya to 245 mya) -- early development of multicellular life
1. Cambrian (to about 500 mya)
2. Ordovician (to about 440 mya)
3. Silurian (to about 410 mya)
4. Devonian (to about 360 mya)
5. Carboniferous (to about 290 mya)
6. Permian (to about 245 mya)
5. Mesozoic (245 mya to 65 mya)
1. Triassic (to about 210 mya)
2. Jurassic (to about 140 mya)
3. Cretaceous (to about 65 mya)
6. Cenozoic (65 mya to present)
1. Tertiary (to about 2 mya)
2. Quaternary (to recent times)
3. the biological record: fossils, comparative anatomy and development, comparative molecular biology
1. DNA-DNA hydridization
2. gene sequencing
2. origins
1. origin of the Earth (Hadean period)
2. orgins of life on Earth
1. What constitutes life on Earth?
1. basic features of all life:  organization, series of chemical reactions (metabolism), reproduction and growth (genetic machinery), responsiveness and homeostasis
2. features of life on Earth:  cellular structure, genetic material consisting of double-stranded DNA, metabolic machinery involving proteins and RNA
2. How did life begin on Earth?
1. early conditions: atmosphere of CO₂, N₂, H₂O, some NH₃ and CH₄, no O₂; the lack of free oxygen may have been crucial
2. build-up of organic molecules led to the formation of a fiarly concentrated primordial soup
1. according to the Oparin-Haldane model, chemical reactions in the atmosphere caused the formation of the more complex molecules (sugars, amino acids); Urey-Miller experiment demonstrated the possibility of forming such molecules in simple systems
2. others, citing problems with the gas mixtures in the Urey-Miller experiment, suggest that precursors molecules were made in deep-sea systems similar to vents in existence today
3. still others contend that the precursors were formed in deep space and came to Earth in comets and meteorites
3. molecules in the primordial soup spontaneously formed more complex structures (proteinoids?, coacervate droplets?)
4. self-replicating structures formed
1. nucleic acids?
1. a quick review of nucleic acids
2. an RNA world?
1. can self-replicate in test-tube
2. can function as organic catalyst
3. somehow became the template for protein production (message, ribosomes, transfer system for amino acids)
2. clay?
5. somehow, the complex structures and the self-regulating structures formed a living structure
1. boundary (this is where proteinoids and droplets come in)
2. metabolic machinery involving enzymes whose formation is directed by RNA
3. energy storage in ATP
4. genetic system to pass information along to the next generation
3. Could this process have been repeated (started) elsewhere in the Solar System?
1. Venus -- probably too hot now and before, closer to the Sun and with a thick CO₂ atmosphere
2. Mars -- now too cold and dry, lacking an atmosphere; in the past more similar to Earth so possible; some claim structures found in a meteorite (AH 84001) thought to have originated on Mars are fossils
3. Jupiter, Saturn, and the other gas giants -- no surface, no liquid water
4. moons of the gas giants
1. Europa (Jupiter)
2. Titan (Saturn)
3. life in the Archean
1. hypothesized structure of early cells
1. cell membrane of phospholipids and proteins
2. DNA-based genetics
3. protein synthesis using ribosomes, tRNA (genetic code)
4. chemoheterotrophic metabolism (fermentation)
5. anaerobic
2. division into distinct lineages (domains of life)
1. Eubacteria
2. Archaea
3. proto-Eukaryotes
3. features and evolution of life in the Archean using Eubacteria as an example
1. cell structure
1. genetic material packaged into a nucleoid (bundled DNA)
2. metabolic machinery based on proteins and RNA (more or less standard; slight differences between eubacterial systems and systems in other domains are the basis of selective antibiotics )
3. cell membrane of phospholipids and proteins (more or less standard)
1. some have complex internal membrane systems to help compartmentalize photosynthesis
4. most have an outer wall containing the peptidoglycan (rigid material of sugar and small proteins)
1. Gram-positive vs Gram-negative walls
2. functions of walls
2. important metabolic features (in the context of the evolution of life)
1. anaerobic vs aerobic
2. chemoheterotroph vs chemoautotroph vs photoautotroph
1. electron-transport chains
2. fermentative vs respiratory heterotrophs
3. non-oxygenic vs oxygenic photoautotrophs
3. nitrogen fixation
3. importance of bacteria in human affairs
1. decomposition
1. sewage treatment
1. primary treatment
2. secondary treatment: sludge digestors/bioreactors; BOD reduction
3. tertiary treatment
2. toxic waste clean-up
3. oil-spills
2. nutrient cycling
1. bacteria-induced redox reactions change solubility of metal ions
1. iron and manganese nodules
2. gold?
2. nitrogen-fixation
3. chemical and food production
4. disease agents
1. types of disease
1. infectious vs non-infectious; contagious
2. viral vs bacterial vs eukaryotic
3. symptoms vs disease
2. Koch's postulates
1. if the putative pathogen is present in all hosts with the disease; and
2. if it can be isolated and cultured; and
3. if it causes the disease when introduced into a healthy host; and
4. it can be reisolated from the now infected host after the disease develeps
5. then the organism is probably the cause of the disease
4. evolution of bacteria
1. sources of variation
1. mutations
2. conjugation
3. transduction
4. transformation
2. hypothesized pattern of evolution
1. anaerobic respiration (electron-transport chains)
2. chemoautotrophy
3. anoxygenic photoautotrophy -- purple-sulfur bacteria and others
4. nitrogen-fixation
5. oxygenic photoautotrophy (chlorophyll-based photosynthesis) -- cyanobacteria
5. evolution of oxygenic photosynthesis -- the end of the Archean

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