Understanding Evolution Evolution Course Needs to Covered 1.Origin of Life- Spontaneous generation; 2.Pasteur and Miller experiments; 3. Introduction to cell and cell organelles Question for Thought •Earth has millions of other kinds of organisms of every imaginable shape, size, and habitat. • This variety of living things is called biological diversity. •How did all these different organisms arise? • How are they related? Who was Charles Darwin? Born: February 12,1809 Birthplace: The Mount, Shrewsbury, England Died: April 19,1882 Cause of death: unspecified Remains: Buried, Westminster Abbey, London, England Darwin’s Theory of Evolution Voyage of Beagle Voyage of the H.M.S. Beagle Darwin's Journal of researches, now known as Voyage of the Beagle, was his first book. As Darwin later recalled in his autobiography 'The voyage of the Beagle has been by far the most important event in my life and has determined my whole career'. He went on to write: As far as I can judge of myself I worked to the utmost during the voyage from the mere pleasure of investigation, and from my strong desire to add a few facts to the great mass of facts in natural science. But I was also ambitious to take a fair place among scientific men... How do you think Darwin came up with his theory? Pattern of Diversity Patterns of Diversity Living Organisms and Fossils As Darwin studied fossils, new questions arose. u Why had so many of these species disappeared? u How were they related to living species? The Galapagos Island Darwin noticed that different tortoise species lived on islands with different environments. He realized that the tortoises had traits that allowed them to live in their particular environments. For example, tortoises that ate plants near the ground had rounded shells and shorter necks. n The smallest, lowest islands were hot, dry, and nearly barren-Hood Island-sparse vegetation n The higher islands had greater rainfall and a different assortment of plants and animals-IsabelaIsland had rich vegetation. The Galapagos Island’s Questions n Darwin was fascinated in particular by the land tortoises and marine iguanas in the Galápagos. n Giant tortoises varied in predictable ways from one island to another. n The shape of a tortoise's shell could be used to identify which island a particular tortoise inhabited. n Land Tortoises n Darwin Finches n Blue-Footed Booby n Marine Iguanas The Journey Home Ideas that shaped Darwin’s Thinking Ideas that Shaped Darwin’s Thinking Lyell argued that the formation of Earth's crust took place through countless small changes occurring over vast periods of time, all according to known natural laws. His "uniformitarian" proposal was that the forces molding the planet today have operated continuously throughout its history Uniform Processes of Change The ideas of Hutton and Lyell led to an understanding of “the rock cycle” as we know it today Charles Bonnet n Born: 13-Mar-1720 Birthplace: Geneva, Switzerland Location of death: Switzerland Cause of death: unspecified n Executive summary: Discovered parthenogenesis Parthenogenesis means that a mother insect can have babies without a father insect. Lamarck’s Contribution n n Jean Baptiste Lamarck was the first to coin the term “Biology” in 1802. He believed that this term would permit botanists and zoologists to share, what life had in common. 1744-1829 n 14 August 1809, presented the two volumes of his most important book, Philosophie Zoologique, to France's Institute National des Sciences et Arts. n Twenty years later, he died penniless, blind and scorned, surrounded by hundreds of unsold copies of his book. n He was buried in a rented plot, exhumed and 'dispersed' five years later. Lamarck’s Theory of Evolution n Tendency towards Perfection(Giraffe necks) n Use and Disuse (bird’s using beaks) n Inheritance of Acquired Traits Population Growth n n Thomas Malthus- 19th century English economist If population grew (more Babies born than die) u Insufficient living space u Food runs out u Darwin applied this theory to animals Alfred Russell Wallace n Born: January 8, 1823 n Birthplace: Great Britain n Died: November 7 1913 n Location of death: England Co -Discovered Theory of Evolution Publication of Origin of Species n Russell Wallace wrote an essay summarizing evolutionary change from his fieldwork in Malaysia n Gave Darwin the drive to publish his findings Natural Selection & Artificial Selection Natural Selection Evolution by Natural Selection Descent n n Descent with Modification-Each living organism has descended, with changes from other species over time Common Descent- were derived from common ancestors Evidence of Evolution Homologous Structures Evidence for Evolution Similarities in Early Development Summary of Darwin’s Theory n Individuals in nature differ from one another n Organisms in nature produce more offspring than can survive, and many of those who do not survive do not reproduce. n Because more organisms are produce than can survive, each species must struggle for resources n Each organism is unique, each has advantages and disadvantages in the struggle for existence n Individuals best suited for the environment survive and reproduce most successful Species change over time n Summary of Darwin’s Theory In evolutionary biology, an evolutionary arms race is an ongoing struggle between competing sets of co-evolving genes, phenotypic and behavioral traits that develop escalating adaptations and counter-adaptations against each other, resembling the geopolitical concept of an arms race. The Escape of the Pathogens: an evolutionary arms race Human populations are constantly locked in evolutionary arms races with pathogens that invade our bodies. We must recognize that these pathogens (such as the Coronavirus) are continuously evolving entities in order to develop better ways to fight them and control their evolution. Mitochondrial Eve is the female ancestor of all human beings. The reason is that the mitochondrial DNA passes on only to mothers to children, and the father has no role. Is Darwin’s theory the only Major One? What are other theories? The Cambrian explosion was a moment of incredible diversification of early life, but it may have been a very rapid moment New protein New function New life Possibility of What is the probability of a functional protein existing by chance? Protein of 150 aa Peptide Bond Success (1:2) D vs L isomer success 1:20 Imagine a protein of 150 aa What is chance factor? Evolution and the origins of life November 20, 2023 Resilience and Perseverance: Understand that setbacks are a part of any journey, be it in sports or academics. Learn to bounce back from failures and setbacks with renewed determination. Teamwork and Collaboration: Cricket is a team sport, and success depends on the collective effort of the team. Similarly, in academic pursuits, collaborating with peers and working as a team can lead to greater achievements. Continuous Improvement: Analyze the performance, identify weaknesses, and work on continuous improvement. In academics, regularly assess your strengths and weaknesses and strive for ongoing personal and academic development. Adaptability and Flexibility: Cricket strategies can change based on the opponent and match conditions. Similarly, in academic life, be adaptable to different teaching styles, learning methods, and unexpected challenges. Maintaining Focus Amid Distractions: In a high-stakes match, focus is crucial. Distractions can lead to errors. Similarly, in college life, staying focused on academic goals amid various distractions is essential for success. Balancing Priorities: Cricket players balance their physical fitness, skills, and mental well-being. As a student, striking a balance between academics, extracurricular activities, and personal well-being is vital. Learn from Mistakes: Analyze mistakes made in the match and use them as learning opportunities. Similarly, in academics, understand and learn from mistakes, whether they are in exams, projects, or other aspects of college life. Sportsmanship and Grace in Defeat: Accept defeat with grace and sportsmanship. Apply the same attitude to academic challenges, understanding that not every endeavor will result in immediate success. Goal Setting and Long-Term Vision: Cricket teams set goals for tournaments, with a long-term vision in mind. As a student, set academic and personal goals with a vision for your overall growth and success. Support System: Cricket teams have a strong support system, including coaches, teammates, and fans. Build a support system in college, including professors, classmates, and friends, to help navigate challenges and celebrate successes together. •Origin of Life • Environmental conditions of primitive Earth • Earth was “born” about 4.5 Billion Years Before Present (Bybp) • The planets probably formed from debris cast off from our Sun following its condensation from interstellar gas and dust of a nebula about 5–7 Bybp • At first, Earth was semi-molten, but gradually cooled enough to form a solid rock crust • The oldest rocks are 3.964 Bybp—from Canada <4.44 billion years ago ere h p os m t a Hydrodynamic gas loss Mode r Degassing n at C on tine oce an th Li nt a l ere Cr u st ric man tle Convecting mantle lid o S Atmospheremagma ocean equilibrium mo sph os Impact degassing ph e Ma gma M iv e s as rly a e Today Mid-ocean ridge Undegassed material? Core Ocean island • As the rate of radioactive decay slowed, water vapor condensed and fell through the atmosphere, dissolving gases and forming a “poisonous” rain • Run-off of rainwater from the land carried dissolved minerals into a shallow proto-ocean • The collective materials in the proto-ocean formed a “hot, thin primordial soup” • Earth’s surface was bombarded by solar energy, especially ultraviolet (UV) radiation (N.B., the ozone layer was not formed until ca. 600 Mybp) • Intense electrical storms generated lightning that assaulted the surface • Together, the UV and lightning provided energy necessary to arrange simple molecules of CH4, NH3, PO4 salts, and H2O into the basic building blocks of organic compounds, and then into complex macromolecules Early gases and water: Origin of life • As Earth cooled, there was a period of intense volcanic activity that released gases into the primitive atmosphere, primarily • • • • • • ammonia = NH3 carbon monoxide = CO hydrogen sulfide = H2S methane = CH4 nitrogen = N2 water vapor = H2O Abiogenesis or the origin of life is the natural process by which life has arisen from non-living matter, such as simple organic compounds Water as a reactant: Water is not just the solvent in which the chemical reactions of living cells occur; it is very often a direct participant in the reactions. The formation of ATP from ADP and inorganic phosphate is an example of a condensation reaction in which the elements of water are eliminated. The reverse of this reaction—cleavage accompanied by the addition of the elements of water—is a hydrolysis reaction. Hydrolysis reactions are also responsible for the enzymatic depolymerization of proteins, carbohydrates, and nucleic acids. Water and carbon dioxide are the end products of the oxidation of fuels such as glucose. The overall reaction can be summarized as The “metabolic water” formed by oxidation of foods and stored fats is actually enough to allow some animals in very dry habitats (gerbils, kangaroo rats, camels) to survive for extended periods without drinking water. The CO2 produced by glucose oxidation is converted in erythrocytes to the more soluble HCO3- , in a reaction catalyzed by the enzyme carbonic anhydrase: In this reaction, water not only is a substrate but also functions in proton transfer by forming a network of hydrogen-bonded water molecules through which proton hopping occurs. Solutes Affect the Colligative Properties of Aqueous Solutions Solutes of all kinds alter certain physical properties of the solvent, water: its vapor pressure, boiling point, melting point (freezing point), and osmotic pressure. These are called colligative (“tied together”) properties. By definition, one of the properties of a solution is a colligative property if it depends only on the ratio of the number of particles of solute and solvent in the solution, not the identity of the solute. The effect of solute concentration on the colligative properties of water is independent of the chemical properties of the solute; it depends only on the number of solute particles (molecules, ions) in a given amount of water. A compound such as NaCl, which dissociates in solution, has twice the effect on osmotic pressure, for example, as does an equal number of moles of a non-dissociating solute such as glucose. Water molecules tend to move from a region of higher water concentration to one of lower water concentration. When two different aqueous solutions are separated by a semipermeable membrane (one that allows the passage of water but not solute molecules), water molecules diffusing from the region of higher water concentration to that of lower water concentration produce osmotic pressure. The chemical evolution of organic molecules (abiogenesis) Life’s First Steps Water and Volcanic Gases Carbon Carbon Monoxide Activated Acetic Acid Oxygen Ammonia Pyruvic Acid Nitrogen Sulfur Alanine Hydrogen Peptide and Water Making amino acids is tricky, even in the laboratory. We know amino acids exist in some kinds of meteorites and interplanetary dust particles. When they rain down on a planet's surface, they import the possible building blocks of life, not necessarily life itself. Scientists think that along the way, there must have been a crucial step that turned atoms into organisms, but they still don't know what it is. In 1953, scientist Stanley Miller performed an experiment that may explain what occurred on primitive Earth billions of years ago. He sent an electrical charge through a flask of a chemical solution of methane, ammonia, hydrogen and water. This created organic compounds including amino acid Abiotic production of biomolecules. Spark-discharge apparatus used by Miller and Urey in experiments demonstrating abiotic formation of organic compounds under primitive atmospheric conditions. After subjection of the gaseous contents of the system to electrical sparks, products were collected by condensation. Biomolecules such as amino acids were among the products. After Miller's death in 2007, scientists examining sealed vials preserved from the original experiments were able to show that there were actually well over 20 different amino acids produced in Miller's original experiments • Life began with the first selfreplicating “organism” • The earliest organism may have been no more than a ribozyme • A ribozyme is an RNA molecule capable of enzymatic actions, e.g., the self-splicing introns of some RNAs, which can excise themselves from the molecule without the help of protein enzymes • Early life forms were continuously bombarded by UV radiation, causing mutations that produced new life forms • As new life forms evolved, the predatory mode appeared • Consumption of prey organisms required catabolism of their organics through the process of respiration • Anaerobic respiration released CO2 into the atmosphere C6H12O6 → energy + C2H3OH + CO2 glucose ethanol carbon dioxide • In the atmosphere, UV radiation cleaved CO2 to form ozone 3CO2 → O3 + 3CO carbon dioxide ozone carbon monoxide UV • The ozone accumulated into the ozone layer in the stratosphere, and blocked most of the UV radiation from penetrating to surface • Formation of the ozone layer enabled development of terrestrial life forms • Other organisms developed the ability to utilize energy released from breaking chemical bonds to manufacture their own organic compounds in the process called chemosynthesis • About 2.7 Bybp, still other organisms developed the ability to utilize energy from sunlight to manufacture their own organic compounds in the process called photosynthesis • Photosynthesis released a new gas into the atmosphere, oxygen CO2 + H2O → C6H12O6 + O2 carbon dioxide water glucose oxygen • At first, all of the oxygen released by photosynthesis reacted with iron in the lithosphere • Gradually, free elements reached oxidized states, and O2 began to accumulate in the atmosphere • Because oxygen interferes with anaerobic respiration, another great change in life occurred, the development of aerobic respiration C6H12O6 + O2 → energy + CO2+H2O Appearance of Eukaryotes Atmospheric pressures of oxygen (atmospheres) • The oxygen-rich atmosphere and aerobic respiration are thought to have led to the evolution of eukaryotes 1.0 0.1 0.01 0.001 0.0001 2.8 2.0 1.0 0 Time (Bypb) The first spike in oxygen levels was a toxic challenge to life and may have shattered a life-sustaining greenhouse. [Adapted from Kerr, 1999]. • Serial Endosymbiosis Theory • In the 1970s, scientists hypothesized that eukaryotes arose as free-living bacteria in symbiosis with some archaebacterial host that became the nucleus-containing cytoplasm of the resulting eukaryote • They further hypothesized that organelles were modified from prokaryotic endosymbionts during eukaryote evolution The Serial Endosymbiotic Theory explains the origin of nucleated eukaryotic cells by a merging of archaebacterial and eubacterial cells. The paradigmatic change is that the driving force behind evolution is not ramification but merging. Lynn Margulis describes the symbiogenetic processes in the language of mechanistic biology in such terms as "merging", "fusion", and "incorporation". Biosemiotics argues that all cell-cell interactions are (rule-governed) sign-mediated interactions, i.e., communication processes. As the description of plant communication demonstrates, the biosemiotic approach is not limited to the level of molecular biology, but is also helpful in examining all sign-mediated interactions between organisms on the phenotypic level. If biosemiotics also uses the notions of "language" and "communication" to describe non-human sign-mediated interactions, then the underlying scientific justification of such usage should be critically considered. • Evidence in support of SET • Some organelles possess their own DNA outside the nucleus of the cell • DNA in organelles is in the form of a convoluted loop • For each organelle, there is an analog that that has been identified among living Eubacteria • Bacteria giving rise to mitochondria were aerobic respirers (and predatory?) • similar to modern α purple bacteria • Bacteria giving rise to plastids were oxygenic phototrophic bacteria • similar to cyanobacteria, and probably were ingested but not digested or digestible • Bacteria giving rise to undulipodia (e.g., cilia, sperm tail, etc., but NOT true flagella of bacteria) • similar to spirochetes Evolution of eukaryotes through endosymbiosis. The earliest eukaryote, an anaerobe, acquired endosymbiotic purple bacteria, which carried with them their capacity for aerobic catabolism and became, over time, mitochondria. When photosynthetic cyanobacteria subsequently became endosymbionts of some aerobic eukaryotes, these cells became the photosynthetic precursors of modern green algae and plants. Eukaryotic Cells Evolved from Simpler Precursors in Several Stages Starting about 1.5 billion years ago, the fossil record begins to show evidence of larger and more complex organisms, probably the earliest eukaryotic cells. Details of the evolutionary path from non-nucleated to nucleated cells cannot be deduced from the fossil record alone, but morphological and biochemical comparisons of modern organisms have suggested a sequence of events consistent with the fossil evidence. Three major changes must have occurred. • First, as cells acquired more DNA, the mechanisms required to fold it compactly into discrete complexes with specific proteins and to divide it equally between daughter cells at cell division became more elaborate. Specialized proteins were required to stabilize folded DNA and to pull the resulting DNA-protein complexes (chromosomes) apart during cell division. • Second, as cells became larger, a system of intracellular membranes developed, including a double membrane surrounding the DNA. This membrane segregated the nuclear process of RNA synthesis on a DNA template from the cytoplasmic process of protein synthesis on ribosomes. • Finally, according to a now widely accepted hypothesis, early eukaryotic cells, which were incapable of photosynthesis or aerobic metabolism, enveloped aerobic bacteria or photosynthetic bacteria to form endosymbiotic associations that eventually became permanent. Some aerobic bacteria evolved into the mitochondria of modern eukaryotes, and some photosynthetic cyanobacteria became the plastids, such as the chloroplasts of green algae, the likely ancestors of modern plant cells. Landmarks in the evolution of life on Earth. At some later stage of evolution, unicellular organisms found it advantageous to cluster together, thereby acquiring greater motility, efficiency, or reproductive success than their free-living single-celled competitors. Further evolution of such clustered organisms led to permanent associations among individual cells and eventually to specialization within the colony. The advantages of cellular specialization led to the evolution of increasingly complex and highly differentiated organisms, in which some cells carried out the sensory functions, others the digestive, photosynthetic, or reproductive functions, and so forth. Many modern multicellular organisms contain hundreds of different cell types, each specialized for a function that supports the entire organism. MULTICELLULAR 0 ANIMALS FUNGI PLANTS UNICELLULAR ARCHAEEUPROTISTS BACTERIA BACTERIA BILLIONS OF YEARS AGO 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 OXYGEN-RICH ATMOSPHERE OXYGEN-FREE ATMOSPHERE ENDOSYMBIONTS PRIMITIVE PHAGOCYTE EUKARYOTES PROKARYOTES COMMON ANCESTRAL FORM Evolutionary transition from a single RNA replicator to a multiple replicator network •Ryo Mizuuchi, Taro Furubayashi & Norikazu Ichihashi Nature Communications volume 13, Article number: 1460 (2022) Cite this article In prebiotic evolution, self-replicating molecules are believed to have evolved into complex living systems by expanding their information and functions open-endedly. Theoretically, such evolutionary complexification could occur through successive appearance of novel replicators that interact with one another to form replication networks. Here we perform long-term evolution experiments of RNA that replicates using a self-encoded RNA replicase. The RNA diversifies into multiple coexisting host and parasite lineages, whose frequencies in the population initially fluctuate and gradually stabilize. The final population, comprising five RNA lineages, forms a replicator network with diverse interactions, including cooperation to help the replication of all other members. These results support the capability of molecular replicators to spontaneously develop complexity through Darwinian evolution, a critical step for the emergence of life. Scientists in Japan have become the first to create an RNA molecule that can replicate, diversify, and develop complexity on its own. Simply put, the molecule can evolve. The RNA replication system. The original host RNA replicates via translation of the self-encoded replicase, by which mutant host RNAs and parasitic RNAs could be generated. b Schematic representation of long-term replication experiments in water-in-oil droplets. (1) RNA replication was performed at 37 °C for 5 h. (2) Droplets were 5-fold diluted with new droplets containing the translation system. (3) Droplets were vigorously mixed to induce their random fusion and division. c Concentration changes of host and parasitic RNAs of different lengths. Host RNA concentrations were measured by RT-qPCR, and parasitic RNA concentrations were measured from corresponding band intensities after gel electrophoresis. Parasitic RNA concentrations were not plotted in rounds where they were undetectable. A possible “RNA world” scenario. RNA or Related Precursors May Have Been the First Genes and Catalysts The RNA world scenario is intellectually satisfying, but it leaves unanswered question: where did the nucleotides needed to make the initial RNA molecules come from? An alternative to this RNA world scenario supposes that simple metabolic pathways evolved first, perhaps at the hot vents in the ocean floor. A set of linked chemical reactions there might have produced precursors, including nucleotides, before the advent of lipid membranes or RNA. Without more experimental evidence, neither of these hypotheses can be disproved. Spontaneous generation THEORY , the hypothetical process by which living organisms develop from nonliving matter; The theory of spontaneous generation, first comprehensively posited by Aristotle in his book ”On the Generation of Animals” around 350 B.C., aims to explain the seemingly sudden emergence of organisms such as rats, flies and maggots within rotting meat and other decomposable items This is incorrect theory In 1668, Francesco Redi, an Italian scientist, designed a scientific experiment to test the spontaneous creation of maggots by placing fresh meat in each of two different jars. One jar was left open; the other was covered with a cloth. John Needham, a microscopist, was a staunch supporter of the aforementioned theory of spontaneous generation, which was the idea that living organisms can develop from non-living matter. Needham's most important experiment claimed that microorganisms in broth developed independently of other cells By sterilizing cultures and keeping them isolated from the open air, Pasteur found that contamination of the media only occurred upon exposure to the outside environment, showing that some element was needed to give rise to life.
