BIO102, Chapt 26

BIO102: Biology of the Organism - single or multicellular, in context with environment

Course Overview - Refer to sylabus

II & III. Animal Biology... Diversity, Physiology, Reproduction & Development, Neurobiology

Lecture I: Where Did Life Come From? Space or Earth?

I. History -- Geological History <<>> Biological History

 

Age of Earth	4.5 billion years	radioisotopic dating of meteorites formed during formation of solar system
Earliest Common Ancestor	3.5-4 billion years	formation of solid crust vs. observation of oldest fossils; carbon isotopes indicate 3.8by metebolic activity (Greenland)
Oldest Prokaryotic Fossils	3.5 billion years	possible cyanobacteria bacteria (autotrophic - photosynthetic). Western Austrailia stromatolites(Fig 26.1)
Oldest Eukaryotic Fossils	2.1 billion years	possible eukarytic algae, Michigan (Han & Runnegar, 1992, Science 257:232) Giardia - "intermediate form" ...two nuclei, no mitochondria
Multicellular Eukaryotes	1-1.2 billion years	projected from on DNA sequence analysis
Cambrian "Explosion" (Animals)	500 million years	Burgess Shale Fossils Many of current animal phyla (echinoderms, annelids, arthropods, chordates). appearance of skeletons thought to be in response to predation. Summary of animal evolution: Fig. 32.3. Summary of chordate evolution: Fig. 34.6.
Origins of Plants from green algae	460 million years	Fossil Record Summary of Plant evolution: Fig. 29.3.
Vascular Plants	400 million years
Gymnosperms	360 million years	"naked seeds", conifers, etc.
Angiosperms	130 million years	"contained seeds", flowering plants
Oldest Vertebrates	500 million years	jawless, fishlike, fig. 34-36
Oldest Jawed Vertebrates	500 million years	Hox gene duplications
Oldest Bony Fishes	425-450 million years
Oldest Amphibians	365 million years	fig. 34-36
Oldest Reptiles	300 million years	fig. 34-36
Oldest Birds	150 million years	fig. 34-36
Oldest Mammals	220 million years	fig. 34-36
Homo erectus	1-2 million years	fig. 34.30, 34.33
Homo sapien	100,000 years	fig. 34.30, 34.33

Age of Earth

1664...James Ussher, Old Testament geneologies, earth is 5668 years old

1800s...James Hutton, Charles Lyell: geological chronology through studies of stratafication


Earth was much older than people had believed
1. Younger rocks deposited on older rocks (superposition)
2. Lavas were originally horizontal
3. Intrusions are younger than host rocks
4. Bolders, etc are older than host rocks
5. Earlier fossils are simpler than more recent forms more recent forms are most similar to existing form

1900s (early) ... Radioisotopic dating gave precise "dates" to strata

II. Biological Evolution:

Darwin - Natural Selection - 1859 (Chapt 22, p. 420)

1. Individuals within species are variable.
....(Variability may or may not be genetically based.)

2. Some of these variations are passed onto offspring.
....(Heritibility is based on variations being based on genetic differences.)

3. In every generation, more offspring are produced than can survive.

4. Survival and reproduction are not random.
....Individuals that survive and reproduce, or who reproduce the most, are those with the most favorable variations. They are naturally selected.
....(Individuals have increased or decreased fitness)

WHAT IS THE PHYLOGENY OF ALL LIVING ORGANISMS

If we have an organism (earliest common ancestor), evolution / natural selection is the mechanism that explains how organisms became increasingly complex and diverse.

Classification of organisms - should be based on evolutionary relationships.


1.5 million extant species (half of these are insects!)
Upper estimate of 30 million species:
Erwin, T.L. (1982) Tropical forests: their richness in coleoptera and other arthropod species. The Coleopterists Bulletin 36, 74-75.

Consider ALL organisms currently extant (as opposed to extinct). Include bacteria, animals, fungi, protozoans, plants... everything. What / When was the Earliest Common Ancestor of ALL life on earth?

Study relationships of ALL known organisms using DNA sequence analysis (Fig. 27.11)


1....Pick a DNA sequence that is common to ALL organisms, incluidng human, bacteria and plants.
2....Pick a DNA sequence that is stable - important function in ALL organisms
3....Pick a DNA sequence that encodes a protein with similar function in ALL organisms

Three Domains:

             |------- Bacteria (Prokaryotes)
             |
Earliest     |
Common ------|   |--- Archaea (extreme prokaryotes)
Ancestor     |   |            (thermophyles, etc.)
             |---|
                 |
                 |--- Eucarya (Nucleus, organelles)
                               Microsporidia, Diplomonads,
                               Trichomonads, Flagellates,
                               Entamoebae, Slime molds,
                               Cilliates, Fungi,
                               Plants, Animals 

Analysis is based on small subunit rRNAs. Support that the Earliest Common Ancestor of ALL extant organisms was "between" the Bacteria and the Archaea/Eucarya is based on using duplicated tRNA genes to root the tree. Arguement is that duplicate tRNA genes are present in all organisms, and therefore the duplications that gave rise to multiple tRNAs MUST have occured BEFORE the derivation of the Earliest Common Ancestor. Therefore, tRNA sequences can serve as a point of comparison of extant organisms with an organism that existed BEFORE the Earliest Common Ancestor.

THE MAJOR EVENTS:
1. Prokaryotic cell organization: membrane, DNA, protein synthesis, metabolic activities

2. Eukaryotic cell organization: nucleus, organelles (endosymbionts) -


DNA sequences (small subunit rRNAs) of mitochondria and chloroplasts are more similar to bacterial homologoues than to nuclear homologues - more latter)

3. Multicellularity, specialization.

Some words on Phylogenetic Trees...(p. 476-485)
These trees represent relationships based on the concept of "lineage by descent". Branches splitting from a common branch point are assumed to have a common ancestor represented by that branch point; the branches are thus (supposed to be) monophyletic. Phylogenetic trees are not necessarily true. They are constructed by choosing a character or several characters that are present in each of the branch tips (taxa) and can thus be compared; differences between character types are used to sort the taxa. There can be many assumptions made in choosing appropriate characters. For example, an untrue tree might be constructed if wings were used as a character and their presence or absence was then used to join birds and insects as closely related taxa. In the tree above, the characters used were nucleotides at corresponding positions within sequences of small subunit tRNA; each nucleotide position was a single character which could be either A G U or C. The phylogenetic trees can only represent time in two ways: (1) if there is some datable fossil record of when two taxa split, and (2) if you are using DNA data and are confident invoking "molecular clock".

Some words on Kingdoms... i.e. plant, animal, etc. (Fig. 26.10)
Kingdoms should be monophyletic. That is, a major lineage that derives from a single common ancestor. We will see, this is not so clearly applied anymore within the Eukaryotes. That is, there may be many Kingdoms within each of the above three domains, based on this criteria. Note that all the groups listed above under Eucarya are monophyletic, suggesting as many as 10 Kingdoms belonging to this Domain

III. Abiotic Evolution

Early atmosphere contained no O₂.
O₂ very reactive, attacks chemical bonds. O₂ not conducive to spontaneous formation of molecules. O₂ atmosphere did not emerge until evolution of photosynthetic process.

1920s A.I. Oparin (Russia) and J.B.S. Haldane (Great Britain) independently postulated that the environmental conditions that originated in primitive earth favored chemical reactions that would synthesize organic compounds from inorganic compounds.

1. Nonbiological processes synthesized organic molecules such as nucleic and amino acids: organic building blocks or "pre-biotic soup"
2. Organic building blocks were assembled into polymers
3. Some combination of these biological polymers was able to self replicate

Once self-replication was "invented", then natural selection could act.

NOTE: O₂ (molecular oxygen) did not appear until photosynthesis had evolved; plants produce O₂ during photosynthesis. EARLY EARTH HAD A REDUCING ATMOSPHERE (NOT AN OXIDIZING ONE).

1. Formation of organic molecules. (See: Lazcano & Miller 1996, Cell 85:793.)


1953 Stanley Miller
In a sealed glass aparatus, he boiled water producing water vapor (H₂0)...
which circulated through atmosphere of methane (CH₄), ammonia (NH₃) and hydrogen (N₂);
in the presence of an electric spark,
and allowed to condense back to water.
Run one week, analyze molecules in water: amino acids glycine and alanine.

Additional experiments by Miller and others: diverse organic molecules, including amino acids, nucleotides, sugars

Presumption was that the early atmosphere contained water, methane, ammonia and hydrogen (No O₂), with energy input from heat and UV radiation.

Concern: some current views suggest CO₂ predominated over CH₄. CO₂ is much less reactive, much more difficult to generate organics using Miller's apparatus. Alternative suggestions are that meteors delivered organics. Early earth was heavily bombarded by meteors, and meteors have been shown to contain carbonaceous compounds. Difficulty is imagining stability during heat of entry.

2. Polymers
Monomeric organic molecules can polymerize through dehydration reactions...
....removal of -H or -OH, condensation and polymerization
Problem - Dehydration Reactions are Highly Reversible
Solution: Catalytic surfaces. Clays stabilize molecules, allowing them to condense and polymerize and stay polymerized.

3. Self replication - Heredity.

First self replicating molecules may have been RNA
Tom Cech (1980s) - rybozymes - non-protein "enzymes"
....edit introns from RNA
....Autocatalytic
Short, single stranded RNA -- can easily fold into 3D structures
....Genotype >> Strucutre >> Phenotype
Current studies aimed at demonstrating that RNA can self replicate and that self replicating RNAs can evolve by natural selection. (Bartel & Szostak,1993, Science 261:1411).

Protobionts - Cell-like Structures

Aggregates of molecules that can maintain internal environment against external environment
Proteinoids + cool H₂O >> microspheres
....microspheres display osmotic swelling, selective permeability
Liposomes ... molecular bilayer
Coacervates ... form from mixtures of polypeptides, nucleic acids, polysaccharaides, shake

Hypothetical Antecedent of Cell
RNA polymers >> hybridization, replication
RNA - amino acid interactions >>> "proteins"
....SELECTION: if some of these proteins act as enzymes, stabilizing RNA replication
Molecuar interaction >> cooperation
First step toward replication & translation
>>>>> energy trapping / transferring molecule
....if held in proximity to replicating RNA, etc. (as in protobionts)
....favor RNA configuration... Natural Selection >>> You!!!!

IV. Life from Space?

Some (e.g. Francis Crick) have argued life is too complicated to have originated under earth conditions, suggest easier to explain if originated elsewhere where conditions might have been more favorable and seeded here by aliens. (Crick & Orgel, 1973. Icarus 19:341.)

Organic molecules / organisms may have been knocked out of another planet in our solar system, such as Mars or Jupiter's moon Europa, by meteor impact, and survived travel to earth. Possible fossils of Martian bacteria observed in Mars derived meteorite (McKay et al., 1996, Science 273:924).

Streptococus mitis (bacteria) survived 2.5 years on moon OUTSIDE unmanned Surveyor 3 probe on moon in foam insulation of a camera (shielded only by camera) (Mitchell & Ellis, 1972, In Analysis of Surveyor 3 Material and Photographs Returned by Apollo 12 (Washington DC: NASA), 239-248.

Spores from a source outside our solar system - would require sheielding. Might survive if shielded by film of carbonaceous material?

NEXT... Prokaryotes and Organismic Diversity...