Unformatted text preview: Clicker Question Alexander Fleming's research on penicillin provides an example of: A) planned methodical research B) the power of large research grants C) an accidental discovery D) hypothesis testing E) the scientific method Where are we? Last time I covered: The nature of scientific discovery. The role of chance in biological research. The Fermi Solution, the power of numbers, and dimensional analysis. That curiosity may be a double-edged sword. This time I am going to discuss: Spontaneous generation Cosmology The origin of life on Earth Life Where did it come from? The Origin of Life The Secret Sits We dance round in a ring and suppose, But the Secret sits in the middle and knows --Robert Frost Where did life originate? Casual observation suggests that living beings can either come from other living beings, or are formed spontaneously. Aristotle believed that plants originated spontaneously from the Earth; frogs and mice sprang up from mud; fireflies came from the morning dew; and mosquitoes, maggots, flies, fleas, bed bugs and lice came from manure, the slime of wells, human excrement, decaying meat and other filth. No Spontaneous Generation Francesco Redi (1668) saw things differently. Redi showed that maggots did not appear in meat if he placed the meat in a jar, and carefully covered it with muslin. In fact, he noticed that maggots did not arise spontaneously, but only developed when flies were allowed to lay their eggs on the meat. No Spontaneous Generation The belief in spontaneous generation of large plants and animals began to wane throughout the seventeenth and eighteenth centuries, due in part, to observations on embryo development by William Harvey, Marcello Malpighi and Pierre Louis Moreau de Maupertuis. Spontaneous Generation of Microbes? With the discovery of microbes by Leeuwenhoek (1677), the belief in the spontaneous generation of microbes, animalicules or living atoms as he called them became the standard belief because the microbes seemed to appear out of nothing. Experimental Proof of Spontaneous Generation of Microbes? The spontaneous generation of microorganisms was confirmed experimentally in 1745 when John Needham boiled chicken broth, stoppered it and found that microbes grew in the boiled broth. But are experimental conclusions always right? Spontaneous Generation Lazzaro Spallanzani (1768) repeated Needham's experiment and showed that if you boiled chicken broth extensively before you stoppered it tightly, microbes would not appear in the broth. They only appeared after the stopper was opened. Microbes only seemed to arise spontaneously because they were ubiquitous. They were either already in any preparation that had not been properly sterilized or were capable of contaminating any preparation that they could enter. Two Interpretations of Spallanzani's Results Spallanzani's supporters believed that he had shown that spontaneous generation was impossible. Needham's supporters believed that Spallanzani had only shown that microbes need air. It was a He Said-He Said situation, until Louis Pasteur came onto the scene with his swanshaped flasks. Pasteur's Swan Shaped Flask that Allowed the Free Movement of Air, but not Microbes No Spontaneous Generation Louis Pasteur (1859), repeated Spallanzani's work. With his now famous swan-shaped flasks that allowed air, but not microbes to pass. Pasteur showed that as long as a solution is properly sterilized (e.g. Pasteurized) and airborne contaminants excluded, no microbes were generated in the broth, even when air was able to freely pass through the long neck. Therefore there is no such thing as spontaneous generation of microbes. Where Did Life Originate? If living organisms can not originate spontaneously, and the early Earth was a molten planet incapable of supporting life, then how did life originate on Earth? Where Did Life Originate? Svente Arrhenius (1908) suggested that if life can not arise spontaneously on Earth, then life must have originated in outer space and come to Earth on meteorites in the form of cosmozoa, microbes, spores or seeds. This theory is called panspermia, which means seeds everywhere. Panspermia Arrhenius (1908) wrote, "The Universe in its essence has always been what it is now. Matter, energy, and life have only varied as to shape and position in space." This sounds very much like- conservation of life! Occam's Razor Occam's Razor: Making the Fewest Number of Hypotheses Even if the panspermia theory be true, we are still faced with the question of how living organisms originated in the Universe and landed on Earth. I will use Occam's razor and assume that life on Earth originated from lifeless matter on Earth itself. Before I discuss the origin of life, I want to start at the beginning and talk about the origin of the universe. How was the Universe Formed? The current consensus among cosmologists is that about 13 billion years ago, space and time as well as all the matter and energy contained in the Universe came into being in one gigantic explosion. This theory is called the big bang theory. The Big Bang Theory According to the modern version of the big bang theory, at time zero, the universe exploded from a infinitesimally tiny and infinitely hot point. According to the big bang theory, and Genesis for that matter, in the beginning there was a unity, a singularity, a primeval atom, as it was called by Lematre. Some people may call it God, others love, intelligence, the spirit of life, consciousness or the unified field. The Big Bang Theory The violent explosion caused the Universe to expand, and as a consequence of the expansion, the Universe began to cool. The Big Bang Theory Between one microsecond and one millisecond after the creation of the Universe, the temperature cooled sufficiently so that energy could be converted into matter in accordance with Einstein's equation: E = mc2. At this point, protons, neutrons and electrons formed, but it was too hot for them to join into atoms. The Big Bang Theory Ten thousand years after the creation of the Universe, it cooled to 10,000 K which is cool enough to allow the association of electrons with protons and neutrons to form hydrogen and helium atoms. The Beginning of Starlight About 10.5-12 billion years ago, the atoms began to coalesce into stars and galaxies as a result of gravitational attraction. As the atoms in the stars were pulled together, the gravitational energy was transformed into radiant energy and the masses of helium and hydrogen began to glow. Stellar Synthesis of the Elements The high temperatures and pressures developed inside the stars provided the energy necessary to fuse the hydrogen into helium and other light elements, including carbon, nitrogen, oxygen, sulfur and phosphorous, the elements so important for life. This is the origin of the abundant elements of life and indeed each of us is made out of stardust. The first generation stars eventually exploded sending fragments of dust into the Universe. The energy of the explosion formed the heavier elements (e.g. iron), which were spread over the Universe in the form of cosmic dust. The Origin of the Solar System Approximately 4.6 billion years ago, on the edge of a spiral galaxy known as the Milky Way, a rotating cloud of gas and dust known as a nebula collapsed, and began to spin faster and faster. The center of the cloud became so massive and dense, it collapsed under gravitational energy and ignited the gasses within it to form our Sun. Around the Sun, other dust particles clumped together into what we now call the planets. One of these clumps formed our home planet, the Earth. Geochemistry of the Early-Earth Four and a half billion years ago the Earth was becoming fully formed. It was extremely hot and essentially ocean-less. The heat was primarily generated by radioactive decay. Geochemistry of the Early-Earth As a result of gravity, the dense nickel and iron sank to the core while the lighter rocky materials containing calcium, magnesium, sodium and potassium, some of the abundant elements that form the body of living organisms, floated to the surface. Atmosphere of the Early-Earth Earthquakes, volcanism and impacts caused gasses in rocks to be released that probably produced an atmosphere of H2O, CO2, N2 as well as CO, CH4, NH3, and H2S. The gravitational attraction of the Earth was not great enough to hold onto the lightest elements, including H2 and He2 and thus most of the original atmosphere of hydrogen and helium was lost. Geochemistry of the Early-Earth Water from outgassing reacted with CO2 in the air to produce carbonic acid (H2CO3). The carbonic acid dissociated into H+ + HCO3-. CO2 + H2O H2CO3 H+ + HCO3(acid) Geochemistry of the Early-Earth Returning to Earth as rain, the carbonic acid probably leached Ca2+ and Mg2+ from rocks, and formed limestone and dolomite. In this way, much of the CO2 was removed from the atmosphere and precipitated in sediments. Atmospheric CO2 would have acted as a greenhouse gas to keep the early-Earth warm. Thus a knowledge of the CO2 concentration would be useful in determining the climate. The actual concentration during the formation of the Earth is not known. Impact Frustration From the formation of the Earth 4.6 billion years ago until approximately 3.8 billion years ago, the Earth was bombarded with fragments of rocks that were not included in the initial process of planet formation. The large fragments may have hit with so much energy that it would have vaporized any organic molecules or living organisms that may have already formed. This is known as the impact frustration theory of the origin of life. Thus from 4.6 to 3.8 billion years ago, life could neither form nor continue on Earth. Oldest Fossils Some of the oldest known rocks formed on Earth, which are 3.5 billion years old, contain fossils that resemble cyanobacteria. Thus prokaryotic-like cells evolved between 3.8 and 3.5 billion years ago, only three hundred million years after the repeated sterilization of the planet by rock fragments from space. Prebiotic Chemical Evolution Matthias Schleiden (1853) thought that it is likely that life originated from the chemicals that existed on Earth. How did complicated carboncontaining compounds, of which living beings exist, originate on Earth? Charles Darwin (1871) guessed that life began in a "warm little pond" when he wrote, "But if (and oh! What a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c present, that a protein compound was chemically formed ready to undergo still more complex changes." Prebiotic Evolution John Burdon Sanderson Haldane (1929), also felt prebiotic evolution was also the mechanism that best explains the origin of life. Prebiotic Evolution "Now, when ultra-violet light acts on a mixture of water, carbon dioxide, and ammonia, a vast variety of organic substances, including sugars and...proteins are built up.... In this present world, such substances, if left about, decay -that is to say, they are destroyed by microorganisms. But before the origin of life they must have accumulated till the primitive oceans had reached the consistency of hot dilute soup." Prebiotic Evolution To test this hypothesis, Melvin Calvin (1951) irradiated a mixture of water and carbon dioxide in a closed chamber with a helium ion beam from the cyclotron. This resulted in the formation of the organic molecules, formic acid and formaldehyde. Prebiotic Synthesis of Carbohydrate (C(H2O)) Prebiotic Evolution Harold Urey, who had been studying the atmosphere of Jupiter, thought that the atmosphere of the early-Earth, may have been more like that of Jupiter, which consisted of hydrogen, methane, ammonia and water. He suggested that Calvin's experiment be repeated using a such an atmosphere. Prebiotic Evolution Stanley Miller created an apparatus designed to mimic this presumed early-Earth condition. A gaseous mixture of methane, ammonia, hydrogen and water was connected to a flask of boiling water. The steam created by the boiling water caused the gasses to move past electrodes, the electrical discharges of which simulated lightning in the atmosphere. A cold water jacket caused molecules to condense and fall out of the "atmosphere". The reaction was allowed to run for a week after which the solution, which had become deep red, was analyzed. Prebiotic Evolution Miller had succeeded in producing not only the formic acid and formaldehyde; but since he included nitrogen, he could also form amino acids, the building blocks of protein. Prebiotic Evolution Under prebiotic conditions amino acids can polymerize into proteins without the aid of enzymes or a template. They do so more readily on the surface of clay. Prebiotic Evolution Sidney Fox heated dry mixtures of amino acids and then placed the mixtures in warm water. Upon cooling, "protocells" are produced. They look similar to the fossils found in rocks that are 3.8 billion years old. Bathybius Haeckelii T. H. Huxley (1868) thought he discovered the primeval proteinaceaous ooze and named it Bathybius Haeckelii. However this "species" turned out to be just gypsum precipitated by alcohol. Prebiotic Evolution Nucleic acids can also be synthesized under early-Earth conditions. Adenine, a component of nucleic acids can be formed by electron irradiation of methane, ammonia and water. Under presumed prebiotic conditions, adenine can also be formed from hydrogen cyanide. The overall reaction is: 5 HCN adenine. HCN, a taker of life to aerobic organisms today, may have been the giver of life billions of years ago. Prebiotic Evolution Ribose and other sugars can also be made under similar conditions by the overall reaction: 5 x formaldehyde (CH2O) ribose (C5H10O5). The adenine and ribose can lose a single water molecule and form adenosine. When inorganic phosphate is added to the prebiotic mix, adenosine trisphosphate (ATP) is formed The components of DNA and RNA can also be formed in the laboratory under presumed earlyEarth conditions. Prebiotic Evolution Low Probability: Miraculous Payoff In the experiments described above, which are performed under presumed earlyEarth conditions, the yields of organic molecules are excruciatingly low and depend greatly on the energy input. While the probability of various molecules coming together in the primordial soup to form a living organism is excruciatingly low, it only had to happen once. Catalysts The chemical reactions I have talked about are extremely inefficient and require a huge input of energy (e.g. ion beams, electric sparks, high temperatures). Catalysts are molecules that reduce the requirement for high energy inputs. Catalysts act by binding two substrates, bringing them together in close proximity and then releasing the product. Enzymes Metals, clays, RNA and proteins are used as catalysts in industrial and biological processes. The proteins, which are polymers of amino acids, are nature's premier catalysts. Each amino acid has a different property for binding substrates. They can be positively charged, negatively charged, polar or nonpolar. The chain of amino acids is flexible enough to bind the substrates and release the product. When proteins act as catalysts, they are called enzymes. Enzymes Allow Reactions to Take Place at Ambient Temperatures Enzymes allow cells to perform chemical reactions at ambient temperatures and under atmospheric pressures. Compare the requirements for nitrogen fixation by the industrial Haber-Bosch process, used to produce fertilizer and the biological process performed by the symbiotic association between bacteria and plants. The Origin of the Genetic Apparatus In order for life to evolve it must replicate with a high yet finite degree of fidelity. Given the complexity of the current genetic apparatus, it is unlikely that the hereditary material arose all at once. Was the original carrier of heredity a protein? A 32 amino acid polypeptide sequence, typically found in a nuclear transcription factor, is capable of replicating itself when supplied with amino acids. Moreover a prion, which is a modified protein that causes infectious diseases such as Mad Cow Disease is able to replicate in the absence of nucleic acids. J. D. Bernal (1951) thinks it is likely that submerged clay-like rocks facilitated the formation of the genetic apparatus due to their ability to adsorb and concentrate molecules. Also see Genesis 2:7 Clay can Replicate As crazy as this idea sounds, clays are capable of replicating themselves. Normally, the composition of a clay crystal is determined by the relative abundance of ions in a solution. However, if a preformed clay particle is put in a suspension of chemicals that would typically form other clays, the growing clays are typical of the seeding clays rather than the suspension. This is because the energy necessary for forming the seed is greater than the energy necessary for growth of the seed. Clay and The Origin of the Genetic Apparatus The clays may have bound nucleotides that were formed during prebiotic conditions. Many nucleotides, including NADH, ATP, UTP and CTP are molecules that activate other molecules and are known as coenzymes. A clay with a particular sequence and density of charge may have bound and ordered a certain linear sequence of nucleotide coenzymes. The Origin of the Genetic Apparatus Such a sequence of coenzymes may have resulted in the performance of sequential activation and binding reactions. On the clay, the sugar phosphates of the nucleotides may have bonded together to form a polymer. The order of the nucleotides may have dictated the sequence of reactions. The Origin of the Genetic Apparatus The nucleic acid polymer has the ability to bind with a "complementary nucleotide" through the formation of hydrogen bonds. The polymer could form an intermediate template so that it could reproduce itself. If the nucleotides reproduced faster than the clays, the nucleic acids would out-compete the clays for the replicating function. This is what Cairns-Smith calls "genetic takeover". The Origin of the Genetic Apparatus Eventually the nucleotides left the evolutionarily-challenged clays behind, and the nucleotide-based genetic code went through its own evolutionary development. The RNA World RNA is the most likely organic candidate for the first self-replicating molecule because it is both an information-bearing molecule and a catalytic molecule. RNA has the ability to replicate itself due to its endogenous polymerase activity. RNA has other catalytic activities. Its OH groups give it the ability to polymerize amino acids. The Chemical Trinity The genetic apparatus probably evolved from RNA alone into the trinity of molecules that carry the information of life: DNA, RNA and protein. DNA and RNA The reactive oxygen atom of RNA is absent in DNA. The Chemical Trinity DNA would be selected for over RNA as an informational molecule because its greater stability. Proteins would be selected over RNA as catalysts because of the variety of functional groups found in the amino acid monomers compared to the nucleotides. Eventually, RNA provided the link between the coding function of DNA, and the catalytic function of proteins. The Formation of Living Cells Molecular complexes, besides those necessary for the genetic apparatus are necessary for life. These includes the molecular complexes involved in energy transformation electrical activity and mechanical movement. The First Common Prokaryotic Ancestor The similarities in molecules, mechanisms, metabolic pathways and structures in plants and animals point to a single common prokaryotic ancestor. The variety of substrates and energy sources available on the early Earth may have resulted in a diversification of the first prokaryotic cell and the formation of many species. Fossil Prokaryotes The Formation of Eukaryotic Cells An ancestral Archaea may have evolved into the host eukaryotic cell containing chloroplasts and mitochondria 1.4 billion years ago. Cyanobacteria are able to convert the sun's energy into readily usable activated nucleotides, including ATP and NADPH. These cyanobacteria may have evolved into the chloroplast. Other prokaryotes convert the chemical energy of organic macromolecules into the chemical energy of the activated nucleotide ATP. These bacteria may have evolved into the mitochondrion. The Evolution of Living Organisms from Single-Celled Organisms Schleiden (1853) wrote, "This view, that the whole fullness of the vegetable world has been gradually developed out of a single cell and its descendants, by gradual formation of varieties, which became stereotyped into species, and then, in like manner, became the producers of new forms, is at least quite as possible as any other, and is perhaps more probable and correspondent than any other, since it carries back the Absolutely Inexplicable, namely the production of Organic Being, into the very narrowest limits which can be imagined." George Wald (1963) captured this awe and rational thinking when he spoke in front of the President of the United States and said, "We have been told so often and on such tremendous authority as to seem to put it beyond question, that the essence of things must remain forever hidden from us; that we must stand forever outside nature, like children with their noses pressed against the glass, able to look in, but unable to enter." "This concept of our origins encourages another view of matter. We are not looking into the universe from outside. We are looking at it from inside. Its history is our history; its stuff, our stuff. From that realization we can take some assurance that what we see is real." "Judging from our experience upon this planet, such a history that begins with elementary particles, leads perhaps inevitably toward a strange and moving end; a creature that knows, a science-making animal that turns back upon the process that generated him and attempts to understand it. Without his like, the universe could be, but not be known, and that is a poor thing. Surely this is a great part of our dignity as men, that we can know, and that through us matter can know itself; that beginning with protons and electrons, out of the womb of time and the vastness of space, we can begin to understand; that organized as in us, the hydrogen, the carbon, the nitrogen, the oxygen, those 16 to 20 elements, the water, the sunlight--all, having become us, can begin to understand what they are, and how they came to be." The Origin of Death If living organisms did not die, the planet would be overcrowded and there would be no room on the planet for younger generations. ...
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- Spring '07