What examples can you think of?

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2 What examples can you think of? Geocentrism Alchemy Heliocentrism: Copernicus, Kepler, Newton, Galileo Nature of the chemical bond (Rutherford, Pauling ) Aristotelian view of the biosphere Woese/Pace (subject of today!) Can you think of others? This is a dynamic process! - Some of these ideas were known and lost, then found again. - We are not done. We can only work with what we understand at the time.

3 Woese and Fox, 1977 All cellular life falls into one of 3 large groups: -Eukaryotes, Eubacteria, Archeabacteria Used 16S rrna sequencing to classify life. This choice of a molecular chronometer was very thoughtful. Why? All life is phylogenetically related on the molecular level! Evolutionary and microbiology connected, microbes are central to studying biosphere

4 Pace, PNAS 2012

5 Technology has changed the way we ask questions in science 16S rrna sequencing in 1977 vs. now are very different. Ribosome: 50% RNA, 50% protein. Small subunit 16S rrna is in all organisms because it s involved in essential function inside cell. It is a marker for relating organisms through evolutionary history, and has changed how evolutionary trees were viewed.

6 What is S? Answer = a unit for sedimentaaon rate

7 Discuss: 1. Why is 16S a good molecule to use for relating organisms? What other molecules can be used for this purpose? 2. Claim: fundamental concepts in biology are rapidly evolving, unlike in physics and chemistry. Do you agree? 3. How to root the tree of life? Universal common ancestor? What do you think of the progenote?

8 Introducing David and Alm paper Summary: The authors analyze distribution of gene families in modern species Gene family: a set of genes which arose from duplication of one gene. Usually code for similar functions. To do this, the authors developed a mathematical/computational model that uses modern genomes to mimic evolution of ancient organisms.

9 Introducing David and Alm paper Conclusions: Ancient environmental change billion years ago caused huge expansion in diversity of genes: 27% of genes today are a result of the evolution that happened during the Archaean expansion. Those genes allowed microbes to make energy from photosynthesis through electron transport. They released a lot of oxygen into the atmosphere, an event for which there is evidence today. Horizontal gene transfer played a big role let s talk about that.

10 Video hhp://glencoe.mcgraw- hill.com/sites/ /student_view0/chapter24/ horizontal_gene_transfer.html

11 Conceptual tree of life with and without extinct lineages Through HORIZONTAL GENE TRANSFER (HGT), molecules from now- exanct lineages might have survived in today's organism. Does this mean anything for 16S RNA sequencing- based tree- making? Zhaxybayeva and Gogarten (2004) Trends in GeneAcs 20 (4)

12 Earth forms ~4.6 bya Oldest evidence for life PhotosyntheAc microbial mats Evidence for oxygen in atmosphere First Eukaryotes Cambrian radiaaon [Time (bya)] PHANEROZOIC Paleozoic Mesozoic Cenozoic 0.6 Ediacaran oldest definite mulacellular life Let s put geological history into perspecave More detailed Ameline: hhp://exploringorigins.org/ameline.html

13 Sketch a geological timeline on a clock 4.6 bya + Today Include the Following: 1. FormaAon of Earth 2. Oldest Evidence for Life 3. PhotosyntheAc Microbial Mats 4. Oxygen in the Atmosphere 5. First Eukaryotes 6. Cambrian RadiaAon Approximate Time: bya bya bya bya bya bya

14 Final questions The difference between two strains of microorganisms is superficially much more subtle than the obvious difference between a person and a flower, but the evolutionary distance between two microbes is often much larger than the distance between humans and plants. What do you think about this? Many questions remain about the best way in which living things can be classified according to their relationships with one another. For example, should the molecular diversity exhibited by microbes be compared on an equal plane with the much more apparent morphological differences found in eukaryotes? What type of classification system do you think makes sense?

15 Pace, PNAS 2012

16 Video and Website Summary of Woese and Pace contributions on the creation of the phylogenetic tree of life option=com_content&view=category&layout=blog&i d=54&itemid=195 Puzzle.html Tree of life with extinct lineages some sequences survive through HGT