Lecture 3: How We Do Science & Evolution PDF

Lecture 3 – How we do Science and its applications to evolution Part 1 – the scientific story is provisional: it changes 2011: How similar are eukaryotes to archaea? (genomes are compared) A comparison of genomes and proteins functional studies suggested similarities between eukaryo...

Lecture 3 – How we do Science and its applications to evolution Part 1 – the scientific story is provisional: it changes 2011: How similar are eukaryotes to archaea? (genomes are compared) A comparison of genomes and proteins functional studies suggested similarities between eukaryotes and the TACK archaea in: Proteins involved in cytokinesis (cell division), cell shape determination, and Protein recycling and membrane remodelling (cellular compartmentalization) A new(ish) view, Hug et al, 2016 A comparison of 92 bacteria phyla, 26 archaeal phyla and all five of the Eukaryotic supergroups based upon the sequences of 16 ribosomal proteins. Three different tresses: which is correct? All of them were: Good simple descriptions of the Theory of Evolution that were consisent with known experimental and observational data at the time. They were all correct at the time The key conclusion: Everything you learn in science is PROVISIONAL and can be overturned or altered by new observations. Part 2 – How do we do Science? Six steps Ancient Greece: Mythos vs Logos A transition in thoughts from Mythos to Logos (rational philosophy and logic).... a precursor to science. Step 1: Science is performed in a rational naturalistic framework Who was the first good scientist? Probably Alhazan, He said vision occurs in the brain, rather than in the eyes. Light travels in straight lines reflects from an object and then into one’s eyes. He stated that a hypothesis must be supported by experiments based on confirmable procedures or mathematical evidence—an early pioneer in the scientific method five centuries before Renaissance scientists Step 2: Experimental/observational support is required Occam’s Razor Step 3: Proceed with the simplest explanation consistent with all the data Repeat, check, compile data: draw conclusions Compile your data, interpret them and draw conclusions  Your dataset will never be complete, so you use inductive reasoning, based upon your data and existing knowledge. Build conceptual models that describe your work Step 4: inductive reasoning allows you to draw conclusions Scientists publish their work... and expect criticism The process: submitting detailed reports of their findings to journals expert (peer reviews) evaluate the validity, design, and relevance of the research. Most papers are returned to authors for revisions or rejections and after improvements, they go through review again. Even after this ~80% of papers are Rejected by the best journals Step 5: Compile and disseminate your knowledge All science is Theory, and Cannot be proved Science is a set of ideas about how the universe works Step 6: Accept uncertainty Part 3: Darwin’s logical inference Evolution – the genetic content of a population changes over time. Microevolution Macroevolution Changes in allele frequencies in a Changes at or above the level of the population of a species over time. species. The three main mechanisms: Natural selection Genetic drift Gene flow How did Darwin get to travel on HMS Beagle (1831-1836)? Darwin spent over 3 years of this trip making observations on land Beagle was Darwin first journey Captain Robert FitzRoy second voyage where he rejected Darwin as companion. Third exploration of Austria Third Voyage Ideas do not come from a vacuum: what influenced Darwin? Darwin had noted variation in nature He thought these were variants of one species: the ornithologist who drew them (John Gould) thought they were a different species. Darwin’s hypothesis, 1859 Darwin’s theory of evolution by natural selection in On The Origin of Species is the logical outcome of these postulates: 1. For any particulate trait, individuals within a species are variable; 2. At least) some of this variation is heritable; 3. Reproduction is not random but is selected by Nature: individuals that reproduce the most are those with the most favorable variations (survival of the fittest).