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2: Origins of life - Biology

2: Origins of life - Biology



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  • 2.1: The Double Helix of DNA
    This structure of DNA was worked out by Francis Crick and James D. Watson in 1953. It revealed how DNA - the molecule that Avery had shown was the physical substance of the genes. It could be replicated and so passed on from generation to generation. For this epochal work, they shared a Nobel Prize in 1962.
  • 2.2: Base Pairing in DNA and RNA
    The rules of base pairing tell us that if we can "read" the sequence of nucleotides on one strand of DNA, we can immediately deduce the complementary sequence on the other strand. The rules of base pairing explain the phenomenon that whatever the amount of adenine (A) in the DNA of an organism, the amount of thymine (T) is the same (called Chargaff's rule). Similarly, whatever the amount of guanine (G), the amount of cytosine (C) is the same.
  • 2.3: The Cell Membrane
    The plasma membrane is referred to as the fluid mosaic model and is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane. These function to identify other cells.
  • 2.4: Comparing Prokaryotic and Eukaryotic Cells
    Cells fall into one of two broad categories: prokaryotic and eukaryotic. The predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro- = before; -karyon- = nucleus). Animal cells, plant cells, fungi, and protists are eukaryotes (eu- = true).
  • 2.5: The Origin of Life
    To account for the origin of life on our earth requires solving several problems: How the organic molecules that define life, e.g. amino acids, nucleotides, were created. How these were assembled into macromolecules, e.g. proteins and nucleic acids, - a process requiring catalysts. How these were able to reproduce themselves. How these were assembled into a system delimited from its surroundings (i.e., a cell). A number of theories address each of these problems.
  • 2.6: First Cells
  • 2.7: Endosymbiosis
    The endosymbiosis theory postulates that the mitochondria of eukaryotes evolved from an aerobic bacterium (probably related to the rickettsias) living within an archaeal host cell and the chloroplasts of red algae, green algae, and plants evolved from an endosymbiotic cyanobacterium living within a mitochondria-containing eukaryotic host cell.

The origin of life

Perhaps the most fundamental and at the same time the least understood biological problem is the origin of life. It is central to many scientific and philosophical problems and to any consideration of extraterrestrial life. Most of the hypotheses of the origin of life will fall into one of four categories:

Hypothesis 1, the traditional contention of theology and some philosophy, is in its most general form not inconsistent with contemporary scientific knowledge, although scientific knowledge is inconsistent with a literal interpretation of the biblical accounts given in chapters 1 and 2 of Genesis and in other religious writings. Hypothesis 2 (not of course inconsistent with 1) was the prevailing opinion for centuries. A typical 17th-century view follows:

[May one] doubt whether, in cheese and timber, worms are generated, or, if beetles and wasps, in cow’s dung, or if butterflies, locusts, shellfish, snails, eels, and suchlike be procreated of putrefied matter, which is apt to receive the form of that creature to which it is by the formative power disposed. To question this is to question reason, sense, and experience. If he doubts of this, let him go to Egypt, and there he will find the fields swarming with mice begot of the mud of the Nylus [Nile], to the great calamity of the inhabitants.

(Alexander Ross, Arcana Microcosmi, 1652.)

It was not until the Renaissance, with its burgeoning interest in anatomy, that such spontaneous generation of animals from putrefying matter was deemed impossible. During the mid-17th century the British physiologist William Harvey, in the course of his studies on the reproduction and development of the king’s deer, discovered that every animal comes from an egg. An Italian biologist, Francesco Redi, established in the latter part of the 17th century that the maggots in meat came from flies’ eggs, deposited on the meat. In the 18th century an Italian priest, Lazzaro Spallanzani, showed that fertilization of eggs by sperm was necessary for the reproduction of mammals. Yet the idea of spontaneous generation died hard. Even though it was clear that large animals developed from fertile eggs, there was still hope that smaller beings, microorganisms, spontaneously generated from debris. Many felt it was obvious that the ubiquitous microscopic creatures generated continually from inorganic matter.

Maggots were prevented from developing on meat by covering it with a flyproof screen. Yet grape juice could not be kept from fermenting by putting over it any netting whatever. Spontaneous generation was the subject of a great controversy between the famous French bacteriologists Louis Pasteur and Félix-Archimède Pouchet in the 1850s. Pasteur triumphantly showed that even the most minute creatures came from “ germs” that floated downward in the air, but that they could be impeded from access to foodstuffs by suitable filtration. Pouchet argued, defensibly, that life must somehow arise from nonliving matter if not, how had life come about in the first place?

Pasteur’s experimental results were definitive: life does not spontaneously appear from nonliving matter. American historian James Strick reviewed the controversies of the late 19th century between evolutionists who supported the idea of “life from non-life” and their responses to Pasteur’s religious view that only the Deity can make life. The microbiological certainty that life always comes from preexisting life in the form of cells inhibited many post-Pasteur scientists from discussions of the origin of life at all. Many were, and still are, reluctant to offend religious sentiment by probing this provocative subject. But the legitimate issues of life’s origin and its relation to religious and scientific thought raised by Strick and other authors, such as the Australian Reg Morrison, persist today and will continue to engender debate.

Toward the end of the 19th century, hypothesis 3 gained currency. Swedish chemist Svante A. Arrhenius suggested that life on Earth arose from “panspermia,” microscopic spores that wafted through space from planet to planet or solar system to solar system by radiation pressure. This idea, of course, avoids rather than solves the problem of the origin of life. It seems extremely unlikely that any live organism could be transported to Earth over interplanetary or, worse yet, interstellar distances without being killed by the combined effects of cold, desiccation in a vacuum, and radiation.

Although English naturalist Charles Darwin did not commit himself on the origin of life, others subscribed to hypothesis 4 more resolutely. The famous British biologist T.H. Huxley in his book Protoplasm: The Physical Basis of Life (1869) and the British physicist John Tyndall in his “Belfast Address” of 1874 both asserted that life could be generated from inorganic chemicals. However, they had extremely vague ideas about how this might be accomplished. The very phrase “organic molecule” implied, especially then, a class of chemicals uniquely of biological origin. Despite the fact that urea and other organic (carbon-hydrogen) molecules had been routinely produced from inorganic chemicals since 1828, the term organic meant “from life” to many scientists and still does. In the following discussion the word organic implies no necessary biological origin. The origin-of-life problem largely reduces to determination of an organic, nonbiological source of certain processes such as the identity maintained by metabolism, growth, and reproduction (i.e., autopoiesis).

Darwin’s attitude was: “It is mere rubbish thinking at present of the origin of life one might as well think of the origin of matter.” The two problems are in fact curiously connected. Indeed, modern astrophysicists do think about the origin of matter. The evidence is convincing that thermonuclear reactions, either in stellar interiors or in supernova explosions, generate all the chemical elements of the periodic table more massive than hydrogen and helium. Supernova explosions and stellar winds then distribute the elements into the interstellar medium, from which subsequent generations of stars and planets form. These thermonuclear processes are frequent and well-documented. Some thermonuclear reactions are more probable than others. These facts lead to the idea that a certain cosmic distribution of the major elements occurs throughout the universe. Some atoms of biological interest, their relative numerical abundances in the universe as a whole, on Earth, and in living organisms are listed in the table. Even though elemental composition varies from star to star, from place to place on Earth, and from organism to organism, these comparisons are instructive: the composition of life is intermediate between the average composition of the universe and the average composition of Earth. Ninety-nine percent of the mass both of the universe and of life is made of six atoms: hydrogen (H), helium (He), carbon (C), nitrogen (N), oxygen (O), and neon (Ne). Might not life on Earth have arisen when Earth’s chemical composition was closer to the average cosmic composition and before subsequent events changed Earth’s gross chemical composition?

Relative abundances of the elements
(percent)
*0 percent here stands for any quantity less than 10 –6 percent.
atom universe life (terrestrial vegetation) Earth (crust)
hydrogen 87 16 3
helium 12 0* 0
carbon 0.03 21 0.1
nitrogen 0.008 3 0.0001
oxygen 0.06 59 49
neon 0.02 0 0
sodium 0.0001 0.01 0.7
magnesium 0.0003 0.04 8
aluminum 0.0002 0.001 2
silicon 0.003 0.1 14
sulfur 0.002 0.02 0.7
phosphorus 0.00003 0.03 0.07
potassium 0.000007 0.1 0.1
argon 0.0004 0 0
calcium 0.0001 0.1 2
iron 0.002 0.005 18

The Jovian planets ( Jupiter, Saturn, Uranus, and Neptune) are much closer to cosmic composition than is Earth. They are largely gaseous, with atmospheres composed principally of hydrogen and helium. Methane, ammonia, neon, and water have been detected in smaller quantities. This circumstance very strongly suggests that the massive Jovian planets formed from material of typical cosmic composition. Because they are so far from the Sun, their upper atmospheres are very cold. Atoms in the upper atmospheres of the massive, cold Jovian planets cannot now escape from their gravitational fields, and escape was probably difficult even during planetary formation.

Earth and the other planets of the inner solar system, however, are much less massive, and most have hotter upper atmospheres. Hydrogen and helium escape from Earth today it may well have been possible for much heavier gases to have escaped during Earth’s formation. Very early in Earth’s history, there was a much larger abundance of hydrogen, which has subsequently been lost to space. Most likely the atoms carbon, nitrogen, and oxygen were present on the early Earth, not in the forms of CO2 (carbon dioxide), N2, and O2 as they are today but rather as their fully saturated hydrides: methane, ammonia, and water. The presence of large quantities of reduced (hydrogen-rich) minerals, such as uraninite and pyrite, that were exposed to the ancient atmosphere in sediments formed over two billion years ago implies that atmospheric conditions then were considerably less oxidizing than they are today.

In the 1920s British geneticist J.B.S. Haldane and Russian biochemist Aleksandr Oparin recognized that the nonbiological production of organic molecules in the present oxygen-rich atmosphere of Earth is highly unlikely but that, if Earth once had more hydrogen-rich conditions, the abiogenic production of organic molecules would have been much more likely. If large quantities of organic matter were somehow synthesized on early Earth, they would not necessarily have left much of a trace today. In the present atmosphere—with 21 percent of oxygen produced by cyanobacterial, algal, and plant photosynthesis—organic molecules would tend, over geological time, to be broken down and oxidized to carbon dioxide, nitrogen, and water. As Darwin recognized, the earliest organisms would have tended to consume any organic matter spontaneously produced prior to the origin of life.

The first experimental simulation of early Earth conditions was carried out in 1953 by a graduate student, Stanley L. Miller, under the guidance of his professor at the University of Chicago, chemist Harold C. Urey. A mixture of methane, ammonia, water vapour, and hydrogen was circulated through a liquid solution and continuously sparked by a corona discharge mounted higher in the apparatus. The discharge was thought to represent lightning flashes. After several days of exposure to sparking, the solution changed colour. Several amino and hydroxy acids, familiar chemicals in contemporary Earth life, were produced by this simple procedure. The experiment is simple enough that the amino acids can readily be detected by paper chromatography by high school students. Ultraviolet light or heat was substituted as an energy source in subsequent experiments. The initial abundances of gases were altered. In many other experiments like this, amino acids were formed in large quantities. On the early Earth much more energy was available in ultraviolet light than from lightning discharges. At long ultraviolet wavelengths, methane, ammonia, water, and hydrogen are all transparent, and much of the solar ultraviolet energy lies in this region of the spectrum. The gas hydrogen sulfide was suggested to be a likely compound relevant to ultraviolet absorption in Earth’s early atmosphere. Amino acids were also produced by long-wavelength ultraviolet irradiation of a mixture of methane, ammonia, water, and hydrogen sulfide. At least some of these amino acid syntheses involved hydrogen cyanide and aldehydes (e.g., formaldehyde) as gaseous intermediates formed from the initial gases. That amino acids, particularly biologically abundant amino acids, are made readily under simulated early Earth conditions is quite remarkable. If oxygen is permitted in these kinds of experiments, no amino acids are formed. This has led to a consensus that hydrogen-rich (or at least oxygen-poor) conditions were necessary for natural organic syntheses prior to the appearance of life.

Under alkaline conditions, and in the presence of inorganic catalysts, formaldehyde spontaneously reacts to form a variety of sugars. The five-carbon sugars fundamental to the formation of nucleic acids, as well as six-carbon sugars such as glucose and fructose, are easily produced. These are common metabolites and structural building blocks in life today. Furthermore, the nucleotide bases and even the biological pigments called porphyrins have been produced in the laboratory under simulated early Earth conditions. Both the details of the experimental synthetic pathways and the question of stability of the small organic molecules produced are vigorously debated. Nevertheless, most, if not all, of the essential building blocks of proteins (amino acids), carbohydrates (sugars), and nucleic acids (nucleotide bases)—that is, the monomers—can be readily produced under conditions thought to have prevailed on Earth in the Archean Eon. The search for the first steps in the origin of life has been transformed from a religious/philosophical exercise to an experimental science.


Lecture notes

1. Describe four processes needed for the spontaneous origin of life on Earth

Process 1: producing organic molecules: synthesis of simple organic molecules from environmental precursors

  • chemical reactions to produce simple organic molecules, such as:
    • amino acids: 20 types
    • nucleotides: purines & pyrimidines
    • monosaccharides: glucose, ribose
    • fatty acids, glycerol
    • water
    • carbon dioxide
    • ammonia

    Process 2: polymerization: assembly of simple organic molecules into polymers

    Process 3: forming a genetic material: formation of polymers that can self-replicate

    • RNA has two key abilities that make it the likely original genetic material
      • genetically: self-replication
        • RNA has been experimentally shown to have the ability to self-replicate
        • RNA nucleotide sequence is variable,
        • allowing for inheritance of information coding for amino acid sequences in polypeptides
        • RNA ribozymes are found in modern cell

        Process 4: producing membranes: packaging the above molecules inside membranes creating an internal chemistry different from their surroundings, including polymers that held the genetic information

        • coacervates
          • a spherical aggregation of macromolecules (proteins, lipids, nucleic acids) making up a colloidal inclusion
          • held together by hydrophobic forces
          • form spontaneously from certain dilute organic solutions
          • 1 to 100 micrometers in diameter
          • possess osmotic properties
          • small spherical aggregations of proteins
          • 2 micrometers in diameter
          • form spontaneously from heated and cooled amino acids
          • exhibit some properties associated with life:
            • response to the environment
            • basic metabolism
            • simple reproduction
            • a spherical vesicle composed of a bilayer membrane
            • form spontaneously from phospholipids

            Result: "protobionts:" the product of the above four processes is likely to have been cell-like structures

            • natural selection is likely to have acted on variants of protobionts competing for resources
            • selecting for:
              • stability: homeostasis, produced by enzymes controlling metabolic reactions
              • longevity: survivorship
              • fidelity: transmitting genetic information with minimal error
              • fecundity: rate of reproduction

              2. Outline the experiments of Miller and Urey into origin of organic compounds

              Simulate reducing atmosphere

              • Miller/Urey: water vapor, hydrogen, methane, ammonia
              • Others: various mixtures w/ carbon dioxide, carbon monoxide, nitrogen, phosphates, etc., and even small amounts of oxygen

              Simulate high energy sources

              • Miller/Urey: mixture of amino acids
              • Others: various mixtures including all 20 amino acids, sugars, lipids, purine and pyrimidine bases of DNA and RNA nucleotides, ATP

              3. State that comets may have delivered organic compounds to Earth.

              • comets contain a variety of organic compounds
                • Murchison meteroite contents are similar to the organic compounds produced by the Miller/Urey experiments
                • could have supplied earth with organic compounds and water

                4. Discuss possible locations where conditions would have allowed the synthesis of organic compounds.

                • deep-sea hydrothermal vents
                  • energy source: heat
                  • spontaneously produces reduced compounds such as iron sulfide
                    • which can be oxidized to synthesize organic molecules
                    • energy source: heat
                    • provides a source of energy for assembly of polymers from monomers
                    • comets
                    • meteorites

                    5. Outline two properties of RNA that would have allowed it to play a role in the origin of life.

                    • RNA has two key abilities that make it the likely original genetic material
                      • genetic: self-replication
                        • RNA has been experimentally shown to have the ability to self-replicate
                          • individual RNA nucleotides self-assemble into RNA polymers
                          • RNA polymers attract complementary nucleotide bases
                            • A=U
                            • G=C
                              • enzymatic: catalyzing chemical reactions
                                • RNA can act as an enzyme, catalyzing various reactions, producing polymers from monomers
                                • in eukaryotic organisms today, RNA regulates numerous cellular functions, including protein synthesis and genetic control
                                • for example, RNA ribozymes are found in modern cell
                                • RNA, like DNA, is a sequence of nucleotides that can carry a genetic code
                                • RNA is structurally simpler than DNA
                                • RNA can self-assemble from nucleotides available from the environment
                                • RNA can self-replicate using an existing RNA molecule as a template, adding free nucleotides available from the environment
                                • copying mistakes = mutations
                                • RNA can enzymatically catalyze metabolic reactions
                                • competition between various RNA varieties selects for most efficient variety

                                6. State that living cells may have been preceded by protobionts, with an internal chemcial environment different from their surroundings.

                                Origins of prokaryotic cells

                                • random collections of organic molecules do not qualify as living, whereas cells do
                                  • life organized as cells requires both organization and stability over time
                                  • cellular structure allows for compartmentalization
                                  • protobionts form compartments which in turn might contain molecules such as RNA capable of reactions, catalysis and replication
                                  • selection would favor the most successful protobionts in terms of stability/survivorship and replication/progeny
                                  • genetic material, probably RNA, would be needed as information for control which could be copied to progeny
                                  • protobionts
                                    • possible origin of membranes
                                    • from aggregates of abiotically produced organic molecules
                                    • a spherical aggregation of lipid molecules making up a colloidal inclusion
                                    • held together by hydrophobic forces
                                    • form spontaneously from certain dilute organic solutions
                                    • 1 to 100 micrometers in diameter
                                    • possess osmotic properties
                                    • small spherical aggregations of proteins
                                    • 2 micrometers in diameter
                                    • form spontaneously from heated and cooled amino acids
                                    • forms a selective membrane
                                    • maintains an osmotic potential
                                    • a spherical vesicle composed of a bilayer membrane
                                    • form spontaneously from phospholipid molecules in turbulent water
                                    • self-assemble into a lipid bilayer forming membrane-bound droplets
                                    • capable of growth and division
                                    • spherical structures containing RNA
                                    • maintaining an internal chemical environment different from their surrounding
                                    • natural selection is likely to have acted on variants of protobionts competing for resources
                                    • selecting for:
                                      • stability: homeostasis, produced by enzymes controlling metabolic reactions
                                      • longevity: survivorship, produced by combinations of metabolic enzymes
                                      • fidelity: transmitting genetic information with minimal error
                                      • fecundity: rate of reproduction

                                      7. Outline the contribution of prokaryotes to the creation of an oxygen-rich atmosphere.

                                      • early cells competing for energy sources are likely to have provided a selection pressure favoring the evolution of photosynthesis
                                        • some photosynthetic prokaryotes use sources of electrons other than water
                                          • photosynthetic prokaryotes that live today in hot springs use hydrogen sulfide as an electron source
                                          • rocks in Greenland dated from 3.7-3.8 billion years ago, called banded iron formations, provide evidence of atmospheric oxygen, suggesting the presence of photosynthetic prokaryotes

                                          8. Discuss the endosymbiotic theory for the origin of eukaryotic cells.


                                          A Brief Update on New Evidence & Theories of LUCA

                                          Allen Nutman and collaborators, studying metacarbonate rocks in the Isua supracrustal belt in southwest Greenland, published the evidence of the oldest known stromatolites (macroscopically layered structures produced by microbial activity), with an age of 3.7 billion years (Nutman et al., 2016). They suggest that the origin of life occurred in shallow marine environments and that ancient organisms were responsible for an autotrophic CO2 inclusion in the ocean (Nutman et al., 2016). In Labrador, Tashiro et al. (2017) found evidence of the oldest biogenic graphite, ≥3.95 billion years old, corresponding to autotrophic organisms in seawater mixed with hydrothermal fluid. This team, led by Japanese geologist Tsuyoshi Komiya, studied carbon isotope values of graphite and carbonate in metasedimentary rocks. Recently, Nutman has been challenged by another team of scientists who studied the same structures present in rocks of Greenland, using a sample close to the original sample site. They concluded that these structures are abiogenic, probably deformed metasediments (Allwood et al., 2018). Recently, Nutman et al. (2019) presented additional examinations supporting the conclusions in their previous study.

                                          Weiss et al. (2016) analyzed 355 genes in bacterial and archaeal phyla. They conceptualized a tree of life as a protein tree representing monophyly of Bacteria and Archaea, from which they inferred the proteins probably present in LUCA, such as reverse gyrase, an enzyme specific of hyperthermophiles, and the Wood-Ljungdahl pathway. Therefore, they suggested that LUCA was an H2-dependent anaerobic autotroph using CO2 and N2, which existed in a hydrothermal environment. Others, such as Dodd et al. (2017), have presented evidence supporting this theory of the origin of life in submarine hydrothermal vents, which occurred at least 3.77–4.28 Ga. The evidence includes fossils of tubes and filaments remains of iron-oxidizing bacteria embedded in rocks of the Nuvvuagittuq belt in Quebec, Canada and the fact that in modern hydrothermal Si-Fe vents, one can find microorganisms that form distinctive tubes and filaments like those in the fossils (Dodd et al., 2017). This idea of the hydrothermal origin of life was first proposed by Corliss et al. (1981) after the discovery of modern submarine hydrothermal vents.

                                          New evidence has also been found in the Dresser Formation, Pilbara Craton, Australia, hot spring deposits within a low-eruptive volcanic caldera (Djokic et al., 2017), which would be a similar environment to the one found presently in Yellowstone National Park (Figure 1). Several “biosignatures” were found, such as evidence of gas bubbles, microbial filaments, and stromatolites (Djokic et al., 2017). The authors proposed a view of the origin of life as occurring in pools that repeatedly dry out and get wet (Djokic et al., 2017 Van Kranendonk et al., 2017). They also performed an experiment using compounds probably available in the prebiotic Earth (nucleic acids) that were put through wet and dry cycles in conditions similar to the hot springs and obtained longer polymers, similar to RNA, encapsulated in protocells (Van Kranendonk et al., 2017). These authors suggest an early environment similar to Darwin’s 1871 hypothesis, noting that “a number of scientists from different fields now think [Darwin] had intuitively hit on something important” (Van Kranendonk et al., 2017, p. 31). Indeed, their evidence supports Darwin’s hypothesis of the origin of life in a warm little pond (Darwin, 1871).


                                          Defining How Life Began

                                          Given all this, scientists can hypothesize how life began on Earth. There is little doubt that mixtures of organic compounds became organized into complex systems by self-assembly processes, because the same thing happens in the organic compounds of meteorites, which are as old as the

                                          The next step occurred when a few of the microscopic systems had the particular set of molecules and properties that allowed them to capture energy and nutrients from the environment, and use them to produce larger polymeric molecules. In the next step toward life, one of the growing systems contained molecules that could be used as templates to direct further growth, so that a second polymeric molecule was in a sense a replica of the first molecule. DNA synthesis in cells is a primary example of molecular growth by polymerization, and also demonstrates how the information in one molecule can be reproduced in a second molecule. Because these processes can be reproduced under laboratory conditions, one can be reasonably certain that they are plausible reactions on the early Earth, even though scientists don't know yet how the first long polymers were produced.

                                          The last step in the origin of life is that one or more of the growing, replicating systems happened to find a way to use the sequence of monomers in one molecule, such as a nucleic acid, to direct the sequence of monomers in another kind of molecule such as a protein. This was the origin of the genetic code and the beginning of life. It also marked the beginning of evolution, because molecular systems composed of two different interacting molecules like nucleic acids and proteins have the potential to undergo mutational change followed by selection.

                                          It is amazing to think that this complex set of events occurred spontaneously on the early Earth, and that life was up and running only a few hundred million years after Earth had cooled sufficiently for liquid water to exist. And yet, this seems to be what happened, and if it happened on Earth it could also happen elsewhere, since the laws of chemistry and physics are believed to be universal. This larger understanding of life has led to a new scientific discipline called astrobiology, which is defined as the study of life in the universe.


                                          Origin of Life: Early Earth Environment

                                          So if Pasteur is correct and life only comes from existing life, where and how did life begin? Many theories attempt to answer this question, including the popular creationist theory, which states that God created man in his own image, which may in fact be correct. However, this section illustrates the scientific evidence that leads to an evolutionary pathway. In the final analysis, both theories may turn out to be the same.

                                          Based on many assumptions, the conditions on early Earth, some three to four billion years ago, are thought to be much different from what they are today. To begin with, the astronomical phenomenon called ?the big bang? is defined by a theory proposing that the earth was one of the larger particles that coalesced after the initial universe explosion, or big bang, that spewed all the particles in the universe away from a central point and destined them to slowly revolve around that point.

                                          Bionote

                                          Iron-containing rocks reportedly recovered from period strata contain no rust, further indicating the absence of oxygen.

                                          Consequently, the earth was very hot, evaporating the liquid water into the atmosphere. However, as the earth cooled, gravity-trapped water vapor condensed, fell as rain, and did not boil away but remained impounded in pools that became lakes and oceans. It was also believed that tectonic activity caused many volcanic eruptions at that time. From present-day volcanoes, we know that when they erupt, they release carbon dioxide, nitrogen, and a host of nonoxygen gases. In addition, with no protecting atmosphere, the earth was constantly bombarded with meteorites and other space debris still in circulation from the big bang. From current astronomical research, we know that meteorites can carry ice and other compounds, including carbon-based compounds. Researchers believe, therefore, that early Earth's atmosphere consisted of water vapor, carbon dioxide, carbon monoxide, hydrogen, nitrogen, ammonia, and methane. Note that no oxygen was present in early Earth's atmosphere!

                                          Meteorologists suspect that lightning, torrential rains, and ultraviolet radiation combined with the intense volcanic activity and constant meteorite bombardment to make early Earth an interesting but inhospitable environment.

                                          Miller-Urey Synthesis

                                          Two American scientists, Stanley Miller and Harold Urey, designed an experiment to simulate conditions on early Earth and observe for the formation of life. They combined methane, water, ammonia, and hydrogen into a container in the approximate concentrations theorized to have existed on early Earth. To simulate lightning, they added an electrical spark. Days later, they examined the ?soup? that formed and discovered the presence of several simple amino acids! Although this experimental design probably did not accurately represent early Earth's percent of gaseous combinations, further work by Dr. Miller and others, using different combinations, all produced organic compounds. As recently as 1995, Miller produced uracil and cytosine, two of the nitrogen bases found in both DNA and RNA. However, to this date, no living things have been made from nonliving things in the laboratory. Interestingly, continuing research on meteorites has identified, as recently as 1969, that they contain all five of the nitrogen bases. This presents the hypothesis that perhaps the ingredients necessary for life were brought from outer space!

                                          Wegener: Plate Tectonics and Continental Drift

                                          By looking at a modern-day map of the world, it is easy to see how the coastline of the west side of Africa appears to match the east coastline of South America. As cartographic skills and knowledge of the continent's boundaries increased by nautical exploration, in 1912, German meteorologist Alfred Wegener proposed an Earth-moving hypothesis. He hypothesized that the existing landmasses are actually moving and probably all began as one large landmass. His theory of continental drift made the landmasses of Earth appear like giant floating islands sometimes moving away, sometimes crashing into each other by forces he could not describe. Although the Africa-South America anomaly was noted, his theory did not gain much support in his lifetime.

                                          Bionote

                                          Most of North America and about one-half of the adjacent Atlantic Ocean ride on the North American plate. The large Pacific plate rubs against the North American plate at the San Andreas fault in Southern California, creating frequent earthquakes.

                                          With recent advances in geology, we now know that all the surface features?land and water?are actually floating on the viscous mantle of the earth, which supports the movable crust and outer layer of Earth. The solid crust, or plate, that we inhabit is one of many irregularly shaped pieces of varying size that move in specified directions. The idea that these large continental plates are in constant motion created by geothermal heating, convection, and movement is called plate tectonics.

                                          Plate tectonics explains how large landmasses separate and also collide into each other. This constant Earth movement, often measured in centimeters per year, is responsible for earthquakes, volcanoes, sea-floor spreading, and continental drift.

                                          Apparently, Wegener was correct the early isolated land forms probably joined together to create a single landmass, or supercontinent called Pangaea, approximately 250 millions years ago at the end of the Paleozoic era. Note in the illustration Pangaea the proposed shape of the supercontinent.

                                          Life that had evolved on the separate landmasses now had to compete with other life-forms from the other isolated landmasses as these landmasses congealed into one. Competition for space, food, and shelter as well as increased predation created additional natural-selection pressures. Fossil records indicate mass extinctions and a major change in genetic diversity at this time.

                                          A second cataclysmic event also affecting biological diversity occurred about 200 million years ago during the Mesozoic era. At that time, Pangaea began to separate, and the isolated land forms again became their own unique isolated evolutionary laboratory. The separating landmasses became reproductively isolated from one another.

                                          Extinction and Genetic Diversity

                                          Extinction appears to be a natural phenomenon and, like natural selection, favors the reproduction of certain species at the expense of less-fit species. Extinction is the loss of all members of a given species and their genetic complement, never to be recovered. Fossil evidence indicates that following a mass extinction such as the Permian extinction, when Pangaea was formed and again at the end of the Cretaceous period when dinosaurs ruled the world, a period of growth and genetic variation followed. Apparently, the extinctions opened the fringe territories for colonization by the remaining species. Mammals are the classic study on this point because they were known to exist 50 to 100 million years in territories inhabited by dinosaurs before the extinction of the dinosaurs. Following the demise of the dinosaurs, mammalian fossils indicate a considerable amount of speciation and growth in overall numbers, both probably associated with the acquisition of new territory and the loss of dinosaurs as competitors and predators.

                                          Bioterms

                                          Adaptive radiation is the process by which genetic diversity is increased in descendants of a common ancestor as they colonize and adapt to new territories.

                                          Adaptive Radiation

                                          The rapid genetic diversity following an extinction, landmass split, or other cataclysmic event may be due to adaptive radiation, also known as divergent evolution.

                                          It is called radiation because the genetically divergent descendants appear to radiate from a central point, much like the solar rays from the sun. During div-ergent evolution, descendants adopt a variety of characteristics that allow them to occupy similarly diverse niches.

                                          The classic example of adaptive radiation is the study completed by Darwin as he observed 13 different finch species during his famous voyage of discovery to the Galapagos Islands. The islands themselves are well suited for adaptive radiation because they consist of numerous small islands in close proximity in the Pacific Ocean approximately 125 miles (200 kilometers) west of Ecuador, South America.

                                          Since Darwin's time, an analysis of the finch speciation revealed a founder population arrived from the mainland and occupied an island. Specific island pressures probably caused that species to evolve into a new species different from the mainland species. As the finches overtook the island, competition increased, and pioneer species may have migrated to a different island. This created a new founder species that adapted to the new island pressures and modified to become a new species. Likewise, the remaining islands were colonized in succession. Because each island is slightly different, the finch adaptations were often unique to a specific island. In addition, finches could return to an inhabited island and compete with the existing species, or return and divide territory, shelter, and resources and peacefully coexist. The return to an inhabited island also probably sparked additional natural-selection pressures.

                                          We are still not sure how life originated on Earth. It could be a heavenly masterpiece, an astronomical anomaly, or a series of mutations and adaptations. There is evidence that favors each theory. Regardless, patterns in similarity appear to link some organisms more closely than others.


                                          Top Five Problems with Current Origin-of-Life Theories

                                          Last summer I published a list of the “Top Ten Problems with Darwinian Evolution.” Since that time, some readers have requested a list of major problems with theories seeking to explain the chemical origin of life. There are numerous problems, but here’s my list of the top 5:

                                          Problem 1: No Viable Mechanism to Generate a Primordial Soup.
                                          According to conventional thinking among origin-of-life theorists, life arose via unguided chemical reactions on the early Earth some 3 to 4 billion years ago. Most theorists believe that there were many steps involved in the origin of life, but the very first step would have involved the production of a primordial soup — a water-based sea of simple organic molecules — out of which life arose. While the existence of this “soup” has been accepted as unquestioned fact for decades, this first step in most origin-of-life theories faces numerous scientific difficulties.

                                          In 1953, a graduate student at the University of Chicago named Stanley Miller, along with his faculty advisor Harold Urey, performed experiments hoping to produce the building blocks of life under natural conditions on the early Earth. 1 These “Miller-Urey experiments” intended to simulate lightning striking the gasses in the early Earth’s atmosphere. After running the experiments and letting the chemical products sit for a period of time, Miller discovered that amino acids — the building blocks of proteins — had been produced.

                                          For decades, these experiments have been hailed as a demonstration that the “building blocks” of life could have arisen under natural, realistic Earthlike conditions, 2 corroborating the primordial soup hypothesis. However, it has also been known for decades that the Earth’s early atmosphere was fundamentally different from the gasses used by Miller and Urey.

                                          The atmosphere used in the Miller-Urey experiments was primarily composed of reducing gasses like methane, ammonia, and high levels of hydrogen. Geochemists now believe that the atmosphere of the early Earth did not contain appreciable amounts of these components. UC Santa Cruz origin-of-life theorist David Deamer explains in the journal Microbiology & Molecular Biology Reviews:

                                          This optimistic picture began to change in the late 1970s, when it became increasingly clear that the early atmosphere was probably volcanic in origin and composition, composed largely of carbon dioxide and nitrogen rather than the mixture of reducing gases assumed by the Miller-Urey model. Carbon dioxide does not support the rich array of synthetic pathways leading to possible monomers… 3

                                          Likewise, an article in the journal Science stated: “Miller and Urey relied on a ‘reducing’ atmosphere, a condition in which molecules are fat with hydrogen atoms. As Miller showed later, he could not make organics in an ‘oxidizing’ atmosphere.” 4 The article put it bluntly: “the early atmosphere looked nothing like the Miller-Urey situation.” 5 Consistent with this, geological studies have not uncovered evidence that a primordial soup once existed. 6

                                          There are good reasons why the Earth’s early atmosphere did not contain high concentrations of methane, ammonia, or other reducing gasses. The Earth’s early atmosphere is thought to have been produced by outgassing from volcanoes, and the composition of those volcanic gasses is related to the chemical properties of the Earth’s inner mantle. Geochemical studies have found that the chemical properties of the Earth’s mantle would have been the same in the past as they are today. 7 But today, volcanic gasses do not contain methane or ammonia, and are not reducing.

                                          A paper in Earth and Planetary Science Letters found that the chemical properties of the Earth’s interior have been essentially constant over Earth’s history, leading to the conclusion that “Life may have found its origins in other environments or by other mechanisms.” 8 So strong is the evidence against pre-biotic synthesis of life’s building blocks that in 1990 the Space Studies Board of the National Research Council recommended that origin-of-life investigators undertake a “reexamination of biological monomer synthesis under primitive Earthlike environments, as revealed in current models of the early Earth.” 9

                                          Because of these difficulties, some leading theorists have abandoned the Miller-Urey experiment and the “primordial soup” theory. In 2010, University College London biochemist Nick Lane stated that the primordial soup theory “doesn’t hold water” and is “past its expiration date.” 10 Instead, he proposes that life arose in undersea hydrothermal vents. But both the hydrothermal vent and primordial soup hypotheses face another major problem.

                                          Problem 2: Forming Polymers Requires Dehydration Synthesis
                                          Assume for a moment that there was some way to produce simple organic molecules on the early Earth. Perhaps they did form a “primordial soup,” or perhaps these molecules arose near some hydrothermal vent. Either way, origin-of-life theorists must then explain how amino acids or other key organic molecules linked up to form long chains (polymers) like proteins (or RNA).

                                          Chemically speaking, however, the last place you’d want to link amino acids into chains would be a vast water-based environment like the “primordial soup” or underwater near a hydrothermal vent. As the National Academy of Sciences acknowledges, “Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored.” 11 In other words, water breaks down protein chains into amino acids (or other constituents), making it very difficult to produce proteins (or other polymers) in the primordial soup.

                                          Problem 3: RNA World Hypothesis Lacks Confirming Evidence
                                          Let’s assume, again, that a primordial sea filled with life’s building blocks did exist on the early Earth, and somehow it formed proteins and other complex organic molecules. Origin-of-life theorists believe that the next step in the origin of life is that — entirely by chance — more and more complex molecules formed until some began to self-replicate. From there, they believe Darwinian natural selection took over, favoring those molecules which were better able to make copies. Eventually, they assume, it became inevitable that these molecules would evolve complex machinery — like that used in today’s genetic code — to survive and reproduce.

                                          Have modern theorists explained how this crucial bridge from inert nonliving chemicals to self-replicating molecular systems took place? Not at all. In fact, even Stanley Miller readily admitted the difficulty of explaining this in Discover Magazine:

                                          Even Miller throws up his hands at certain aspects of it. The first step, making the monomers, that’s easy. We understand it pretty well. But then you have to make the first self-replicating polymers. That’s very easy, he says, the sarcasm fairly dripping. Just like it’s easy to make money in the stock market — all you have to do is buy low and sell high. He laughs. Nobody knows how it’s done. 12

                                          The most prominent hypothesis for the origin of the first life is called the “RNA world.” In living cells, genetic information is carried by DNA, and most cellular functions are performed by proteins. However, RNA is capable of both carrying genetic information and catalyzing some biochemical reactions. As a result, some theorists postulate the first life might have used RNA alone to fulfill all these functions.

                                          But there are many problems with this hypothesis.

                                          For one, the first RNA molecules would have to arise by unguided, non-biological chemical processes. But RNA is not known to assemble without the help of a skilled laboratory chemist intelligently guiding the process. New York University chemist Robert Shapiro critiqued the efforts of those who tried to make RNA in the lab, stating: “The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth.” 13

                                          Second, while RNA has been shown to perform many roles in the cell, there is no evidence that it could perform all the necessary cellular functions currently carried out by proteins. 14

                                          Third, the RNA world hypothesis can’t explain the origin of genetic information.

                                          RNA world advocates suggest that if the first self-replicating life was based upon RNA, it would have required a molecule between 200 and 300 nucleotides in length. 15 However, there are no known chemical or physical laws that dictate the order of those nucleotides. 16 To explain the ordering of nucleotides in the first self-replicating RNA molecule, materialists must rely on sheer chance. But the odds of specifying, say, 250 nucleotides in an RNA molecule by chance is about 1 in 10 150 — below the “universal probability bound,” a term characterizing events whose occurrence is at least remotely possible within the history of the universe. 17 Shapiro puts the problem this way:

                                          The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. … [The probability] is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck. 18

                                          Fourth — and most fundamentally — the RNA world hypothesis can’t explain the origin of the genetic code itself. In order to evolve into the DNA/protein-based life that exists today, the RNA world would need to evolve the ability to convert genetic information into proteins. However, this process of transcription and translation requires a large suite of proteins and molecular machines — which themselves are encoded by genetic information.

                                          All of this poses a chicken-and-egg problem, where essential enzymes and molecular machines are needed to perform the very task that constructs them.

                                          Problem 4: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code.
                                          To appreciate this problem, consider the origin of the first DVD and DVD player. DVDs are rich in information, but without the machinery of a DVD player to read the disk, process its information, and convert it into a picture and sound, the disk would be useless. But what if the instructions for building the first DVD player were only found encoded on a DVD? You could never play the DVD to learn how to build a DVD player. So how did the first disk and DVD player system arise? The answer is obvious: a goal-directed process — intelligent design — is required to produce both the player and the disk.

                                          In living cells, information-carrying molecules (such as DNA or RNA) are like the DVD, and the cellular machinery that reads that information and converts it into proteins is like the DVD player. As in the DVD analogy, genetic information can never be converted into proteins without the proper machinery. Yet in cells, the machines required for processing the genetic information in RNA or DNA are encoded by those same genetic molecules — they perform and direct the very task that builds them.

                                          This system cannot exist unless both the genetic information and transcription/translation machinery are present at the same time, and unless both speak the same language. Not long after the workings of the genetic code were first uncovered, biologist Frank Salisbury explained the problem in a paper in American Biology Teacher:

                                          It’s nice to talk about replicating DNA molecules arising in a soupy sea, but in modern cells this replication requires the presence of suitable enzymes. … [T]he link between DNA and the enzyme is a highly complex one, involving RNA and an enzyme for its synthesis on a DNA template ribosomes enzymes to activate the amino acids and transfer-RNA molecules. … How, in the absence of the final enzyme, could selection act upon DNA and all the mechanisms for replicating it? It’s as though everything must happen at once: the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don’t see them at the moment. 19

                                          The same problem confronts modern RNA world researchers, and it remains unsolved. As two theorists observed in a 2004 article in Cell Biology International:

                                          The nucleotide sequence is also meaningless without a conceptual translative scheme and physical “hardware” capabilities. Ribosomes, tRNAs, aminoacyl tRNA synthetases, and amino acids are all hardware components of the Shannon message “receiver.” But the instructions for this machinery is itself coded in DNA and executed by protein “workers” produced by that machinery. Without the machinery and protein workers, the message cannot be received and understood. And without genetic instruction, the machinery cannot be assembled. 20

                                          Problem 5: No Workable Model for the Origin of Life
                                          Despite decades of work, origin-of-life theorists are at a loss to explain how this system arose. In 2007, Harvard chemist George Whitesides was given the Priestley Medal, the highest award of the American Chemical Society. During his acceptance speech, he offered this stark analysis, reprinted in the respected journal Chemical and Engineering News:

                                          The Origin of Life. This problem is one of the big ones in science. It begins to place life, and us, in the universe. Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea. 21

                                          Many other authors have made similar comments. Massimo Pigliucci states: “[I]t has to be true that we really don’t have a clue how life originated on Earth by natural means.” 22 Or as science writer Gregg Easterbrook wrote in Wired, “What creates life out of the inanimate compounds that make up living things? No one knows. How were the first organisms assembled? Nature hasn’t given us the slightest hint. If anything, the mystery has deepened over time.” 23

                                          Likewise, the aforementioned article in Cell Biology International concludes: “New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood.” 24 That is, they may never be understood unless scientists are willing to consider goal-directed scientific explanations like intelligent design.


                                          The Institute for Creation Research

                                          In the first article "Origin of Life: A Critique of Early Stage Chemical Evolution Theories,", January, 1976, of this series on origin of life theories, following the discussion of problems involved in a naturalistic origin of relatively simple organic compounds, the problem of the origin of large molecules ("macromolecules"), such as the proteins, DNA, and RNA, was introduced. It was pointed out that one of the insuperable barriers to the accumulation of significant quantities of these very complex molecules (even assuming that the ocean was populated with huge quantities of the necessary chemicals) was the fact that energy is required to form the chemical bonds between the units in these long-chain compounds.

                                          FIGURE 1.

                                          As a consequence, there is, practically speaking, no tendency for these compounds to form, but, on the other hand, they very readily tend to fall apart or disintegrate. What happens naturally and spontaneously, then, is that proteins break up into their constituent amino acids, and DNA and RNA tend to break up into fragments, and eventually into their constituent groups -- a sugar, phosphoric acid, and purines and pyrimidines. If proteins, DNA, RNA, and other complex macromolecules arose on the hypothetical primitive earth by naturalistic processes, some mechanism would have had to exist to drive this process in the direction opposite to that which it tends to go. This mechanism would have had to be very efficient, since many billions of tons each of many different kinds of proteins, DNA, and RNA would have to be produced to provide enough of these vital compounds for the origin of life in an ocean containing somewhere between 35 and 350 million cubic miles of water.

                                          Fox's Thermal Model

                                          The suggestion that has gained more attention than all others is the idea of Sidney Fox. Fox has published papers on various aspects of his thermal theory in numerous scientific journals and in many books, a few of which are listed in the bibliography of this paper. 1-5 An outline of Fox's theory can be found in practically every modern high school and college text on biology, evolution, and related subjects. Recently a review volume was published in honor of his 60th birthday. 6 And yet if any thing in science is certain, it can be said that however life arose on this planet, it did not arise according to the scheme suggested by Fox. One could not be judged to be too unkind or critical if he were to label Fox's suggestion as pseudoscience.

                                          Fox uses intense heat as the driving mechanism in his model. In the laboratory demonstration of Fox's origin of life scheme, a particular mixture of pure, dry amino acids are heated at about 175° C (water boils at 100° C) for a limited time (usually about six hours). Intense heating is then ceased, and the product is stirred with hot water, and insoluble material is removed by filtration. When the aqueous solution cools, a product precipitates in the form of microscopic globules, which Fox calls proteinoid microspheres. Analysis of this material shows that it consists of polymers, or chains, of amino acids, although of shorter lengths than are usually found in proteins. Some of these globules resemble coccoid bacteria, and others bulge and superficially appear to be budding similar to certain microorganisms.

                                          Fox claims that his proteinoid microspheres constitute protocells (that is, they are almost, but not quite, true cells), and were a vital link between the primordial chemical environment and true living cells. He claims that the amino acids in these polymers are not randomly arranged as would be expected, but that a few highly homogeneous (having identical chemical structure) protein-like molecules are obtained with their amino acids arranged in a precisely ordered sequence. He further claims that these compounds possess detectable catalytic or enzyme-like properties. Finally, Fox claims that these microspheres multiply by division somewhat in the manner of true cells.

                                          FIGURE 2.The above reaction represents the formation of dipeptide, which contains only two amino acids. The average protein contains several hundred amino acid residues. To form such a protein, the above reaction would be repeated many times as the amino acids are added successively to the end of the chain.

                                          When asked where on the primordial earth a locale could be found where amino acids might have been heated at about 175° C, Fox suggests that such a locale would have been found on the edges of volcanoes. When it was pointed out that heating at that high a temperature (not much reaction occurs at temperatures much below 175° C) would cause complete destruction of the products if heating continues much beyond six hours, Fox suggests that rain might occur just at the right time to wash away the products.

                                          Fox's scheme would require such a unique series of events and conditions, the probability of which would be so vanishingly small that it could be equated to zero. These are the following:

                                          1. Heating at a high temperature for a limited amount of time.

                                          Fox's suggestion that the combination of the edges of volcanoes with rain at just the right time would suffice to produce billions of tons of these polymers has been severely criticized even by numerous evolutionists. 7 Miller and Orgel point out that when lava solidifies, the surface of the lava is hardly warmer than air temperature. In discussing this feature of Fox's model they say, "Another way of examining this problem is by asking whether there are places on the earth today with appropriate temperatures where we could drop, say, 10 grams of a mixture of amino acids, and obtain a significant yield of polypeptides&hellip We cannot think of a single such place." 8 Even if there were such places, they would be so limited in extent, and the timing of the rain would be so restrictive (not much less nor much more than six hours from the time heating begins), that the rate of production would be very much less than the rate of destruction by hydrolysis and other degradative reactions once the products were washed into the ocean or other bodies of water.

                                          2. Fox's reaction mixture consists solely (as far as organic material is concerned) of pure amino acids.

                                          Where on earth could a mixture of pure amino acids be found? Only in the laboratory of a twentieth-century scientist! According to the chemical evolutionary scheme to which Fox and every other origin of life theorist subscribes, however, a great variety of organic chemical compounds, numbering in the thousands and most likely many tens of thousands, would have been produced on the primordial earth. The probability of a mixture of pure amino acids accumulating anywhere, assuming that they were being produced, would be absolute zero. Any amino acids produced would be admixed with sugars, aldehydes, ketones, carboxylic acids, amines, purines, pyrimidines, and other organic chemicals. Heating amino acids at almost any temperature with a mixture of such chemicals would be certain to result in complete destruction of the amino acids. Beyond question, no polypeptides or proteinoids would be produced. This factor alone completely eliminates Fox's scheme from any rational discussion.

                                          3. A totally improbable ratio of amino acids is required.

                                          If random proportions of amino acids are heated, no product is obtained. A very high proportion of one of the acidic amino acids, aspartic and glutamic acids, or of the basic amino acid, lysine, is required. Generally, about one part of one of the acidic amino acids, or one part of lysine, a basic amino acid, is heated with two parts of all the remaining amino acids combined. Under no naturally occurring conditions would any such ratio of amino acids ever exist. In all origin of life laboratory experiments, the amino acids produced in highest ratios are glycine and alanine, the simplest in structure and therefore the most stable of all the amino acids. Aspartic and glutamic acids are generally produced, but in small proportions. Detectable quantities of lysine are rarely, if ever, produced. Again, Fox's scheme is completely out of touch with reality.

                                          4. Serine and threonine are mainly destroyed.

                                          Two of the most commonly occurring amino acids in proteins consist of serine and threonine. Yet they undergo severe destruction during the heating process required in Fox's scheme. The resultant product thus contains only minor amounts of serine and threonine in contrast to naturally occurring proteins.

                                          5. The claim that the products consist of a few relatively homogeneous polypeptides ("proteinoids") with amino acids arranged in a highly ordered sequence is patently absurd.

                                          If a monkey were allowed to type away on a typewriter, the sequence in the string of letters produced on the paper would be completely random. The result would be nonsense. So it is with polymers produced from amino acids, nucleotides, or sugars according to ordinary chemical and physical processes. Chemistry and physics, just like monkeys, are dumb things, and have no ability to arrange subunits in any particular order. Probability considerations based on relative reactivities of functional groups and activation energies require the production of random structures or sequences in any polymerizations involving mixtures of amino acids, nucleotides, or sugars. It has been demonstrated that, in fact, polymerization of sugars 9 and of nucleotides 10 leads to random sequences.

                                          Fox's claim that his product consists of relatively large quantities of a few polypeptides (polymers of amino acids are called polypeptides when the chains are shorter than proteins), each with the amino acids arranged in a highly specific sequence, rather than an enormous number of polypeptides with random structures, is based upon entirely inadequate separation techniques and analyses. There is no valid evidence whatever to show whether or not the amino acids in Fox's products are ordered. In fact, some of his fellow origin of life theorists accuse Fox of deception in this respect. Thus, Miller and Orgel, concerning Fox's claim that his product consists of nonrandom polypeptides, say "Thus, the degree of nonrandomness in thermal polypeptides so far demonstrated is minute compared with the non-randomness in proteins. It is deceptive, then, to suggest that thermal polypeptides are similar to proteins in their nonrandomness." 11

                                          Beyond the above considerations, there is additional compelling evidence that Fox's product must consist of random structures. The high temperature required for the reaction nearly completely racemizes the amino acids. All but one of the amino acids found in proteins (glycine is the exception) may exist in at least two forms, forms in which the arrangement in space of the atoms differ. These forms are designated as the D- and L- forms (sometimes called "right-" and "left-handed"). They bear the same relationship to each other that a right hand bears to a left hand each is a mirror-image of the other but not superimposable. Chemically and physically they exhibit identical properties except that solutions of the two forms rotate plane-polarized light in opposite directions. Biologically the difference is enormous, however. All naturally occurring proteins contain exclusively the L-, or "left-handed," form. The replacement of a single amino acid in a protein with its D-form completely destroys all biological activity.

                                          FIGURE 3.The amino acid sequence of the protein chymotrypsinogen.

                                          Racemization is the process which converts D-amino acids to a mixture of the D- and L-forms, or L-amino acids to a mixture of the D- and L-forms. When an amino acid is completely racemized it consists of equal quantities of the D- and L-forms. All amino acids tend to racemize under natural conditions, the rate of racemization depending on the particular amino acid and environmental conditions. The brutal treatment of heating amino acids several hours at 175° C, as mentioned above, extensively racemizes the amino acids, changing the amino acids from L-forms to a mixture of L- and D-forms.

                                          Since the D- and L-forms of amino acids have identical chemical properties, the probability of the D-form being incorporated at any point in the chain is equal to the probability of the incorporation of the L-form. There would be no way then, chemically, of specifying which form would be incorporated at any particular point. The sequence of the first two amino acids in the chain might thus be L-L, D-D, D-L, or L-D. Each would have equal probability. The sequence of the first three amino acids, whatever the particular amino acids, might be L-L-L, L-L-D, L-D-L, L-D-D, D-D-D, D-D-L, D-L-D, or D-L-L. Thus, it can be seen that even if the sequence of the first three amino acids were the same (such as, for example, arginine-valine-threonine), eight different structures can be obtained, differences which would exert enormous influence biologically. In fact, based on known bio-chemistry, only the L-L-L form could have had any potential significance.

                                          It is thus impossible for Fox's product to consist of specific structures. A particular sequence of ten amino acids but consisting of mixtures of the D- and L-forms would yield a thousand different structures (2 10 ) and a particular sequence of 100 amino acids existing in D- and L-forms would yield 10 billion times 10 billion times 10 billion different structures (2 100 or approximately 10 30 ). It is apparent that Fox's claim for a high degree of homogeneity, or non-randomness, in his product is indeed absurd.

                                          6. Catalytic, or enzymic, properties claimed for the product are barely detectable and unrelated to present enzymes.

                                          The catalytic properties of enzymes found in present-day organisms are due to the precise sequence of the L-amino acids in these proteins. Fox's product consists of random sequences of these amino acids. Any enhancement of the catalytic activity of the free amino acids themselves by this polymerization would be no more than that conveyed by the incorporation of these amino acids into random polymers or nonspecific chemical structures. Furthermore, these polymers consist of mixtures of D- and L-amino acids. As mentioned earlier, the substitution of only one L-amino acid by its D-form in an enzyme (which may consist of several hundred amino acids) completely demolishes, for all practical purposes, its biological, that is, its catalytic, ability (residual activity, if any, is reduced below a detectable quantity). Further discussion of this point may be found in the monograph by Gish on the origin of life. 12 It is probable that if Fox had swept up the dust on the floor of the university administration building and thrown it into his test mixture, it would have had as much activity as his proteinoid.

                                          7. The proteinoid microspheres are unstable and are easily destroyed.

                                          Fox claims a rather high degree of stability for his proteinoid microspheres, yet he, himself, reveals that microspheres contained in aqueous suspension between microscope slides can be easily redissolved by merely warming the slides. 13 Stable, indeed! Furthermore, dilution of an aqueous suspension by adding water also dissolves the microspheres.

                                          8. Division of the microspheres is due to simple physicochemical phenomena and have no relation to cell division by living organisms.

                                          Cell division in even the simplest organisms requires an incredibly complex process and machinery, involving duplication of each unit of the cell with extremely high fidelity. On the other hand, the division reported for Fox's microspheres is a simple physicochemical phenomenon, like the separation of a soap bubble into two bubbles. It has no greater significance. As material precipitates from solution in the form of globules, and as the quantity that has collected in any particular globule exceeds a certain amount, physicochemical forces may cause the globule to split into two globules. No reproduction, no replication of any kind, however, takes place. The material in the first globule would be randomly distributed between the two product globules.

                                          This discussion of the Fox scheme for the origin of life, even though incomplete, has been relatively extensive. This is believed desirable, however, because of the tremendous promotion (and naive acceptance) of Fox's theories in high school and college texts and in scientific circles as well. Fox's success confirms the bias and unscientific attitudes that dominate the educational and scientific establishments in relation to the question of origins. Anything that incorporates evolutionary philosophy is acceptable, no matter how unscientific.

                                          Other Models

                                          Other suggestions have been offered (good but concise reviews of these may be found in the paper by Horowitz and Hubbard 7b and the book by Miller and Orgel 7a ). Those that involve reactions in aqueous solution (and thus in the oceans, lakes, and all other aqueous environments) can be effectively eliminated because the high energy reagents required to provide the energy to form the chemical bonds between the amino acids, nucleotides, etc., would be rapidly destroyed by water. These reagents are effective in laboratory syntheses because the reagents are prepared in non-aqueous solvents under anhydrous conditions, and the reactions in which these reagents are used are generally carried out under similar conditions. There is no possibility that these reagents could form on the primitive earth, however.

                                          Other suggestions utilizing elevated temperatures in a dry environment, in addition to the suggestion of Fox, have been offered. 14 Orgel and his collaborators have published a series of papers, for example, on the thermal synthesis in a dry environment of nucleotides and of polymers of nucleotides, 15 but Orgel, himself, admits that these experiments have no relevance to the origin of life. After discussing the possibilities of such reactions occurring under primitive earth conditions, Miller and Orgel state, "However, we doubt that very extensive polymerization of nucleotides could have occurred in this way, or that 'biological' polymerization could have taken place except in an aqueous environment." 16

                                          Miller and Orgel have thus stated their conviction that polymerizations that gave rise to proteins, DNA, RNA, and other biological molecules ("&lsquobiological&rsquo polymerizations") must have occurred in an aqueous environment. But as stated above, this would have been impossible because the high energy compounds needed to drive these polymerization reactions could not have formed or existed in an aqueous environment.

                                          In the concluding paragraph to their chapter on polymerizations, Miller and Orgel state, "This chapter has probably been confusing to the reader. We believe this is because of the very limited progress that has been made in the study of prebiotic condensation reactions." 17 This lack of success has resulted from the extreme difficulties in attempting to imagine how such processes could have occurred under natural conditions. Some might suppose, on the other hand, that limited progress has been made mainly because comparatively little research has yet been done on the origin of life. In that limited amount of research, however, enough work has been done to test all principles involved. Further work will not alter the principles of thermodynamics, chemical kinetics, or other basic principles involved. These stand as barriers to a naturalistic origin of biologically active molecules.

                                          This series on origin-of-life theories will be concluded in a future issue.


                                          2: Origins of life - Biology

                                          Lecture Description

                                          This video lecture, part of the series Useful Genetics by Prof. Rosie Redfield, does not currently have a detailed description and video lecture title. If you have watched this lecture and know what it is about, particularly what Biology topics are discussed, please help us by commenting on this video with your suggested description and title. Many thanks from,

                                          - The CosmoLearning Team

                                          Course Index

                                          1. Overview of Module 1
                                          2. How different are we?
                                          3. Properties of DNA
                                          4. Properties of genes
                                          5. Why molecular biology is confusing
                                          6. Properties of chromosomes
                                          7. Life cycles and ploidy
                                          8. Comparing DNA sequences
                                          9. Genetic and evolutionary relationships of human populations
                                          10. Overview of Module 2
                                          11. Fidelity of DNA replication
                                          12. Why most mutations are harmless
                                          13. Types of mutations and their consequences
                                          14. Germline and Somatic Mutations
                                          15. Mutagens (what should we worry about)
                                          16. Mutations, selection and evolvability
                                          17. Origins and evolution of new genes and gene families
                                          18. Comparing DNA sequences reveals evolutionary history
                                          19. Overview of Module 3
                                          20. Protein basics
                                          21. Catalytic proteins (enzymes)
                                          22. Structural, transport and carrier proteins
                                          23. Regulatory proteins and RNAs
                                          24. Homozygous phenotypes
                                          25. Diploids: Heterozygous phenotypes
                                          26. All about dominance
                                          27. How genes are named
                                          28. Gene interaction in biochemical pathways
                                          29. Regulatory interactions
                                          30. How somatic mutations cause cancer
                                          31. Frameworks for predicting the phenotypic effects of mutation
                                          32. Overview of Module 4
                                          33. Sex chromosomes and sex determination
                                          34. Expression of X‐linked genes in females
                                          35. Expression of X‐linked genes in males
                                          36. Can natural genetic variation explain natural phenotypic variation?
                                          37. Most natural variation has very small effects
                                          38. Many natural genetic variants affect multiple traits
                                          39. Effects of natural genetic variation depend on the environment
                                          40. Effects of natural genetic variation depend on chance
                                          41. How natural genetic variation affects the risk of cancer
                                          42. Integrating new understanding into old concepts
                                          43. Overview of Module 5
                                          44. DNA fingerprinting
                                          45. Analyzing a single gene or gene 'panel'
                                          46. SNP-typing the genome, Part 1
                                          47. SNP-typing the genome, Part 2
                                          48. SNP-typing services
                                          49. Exome sequencing
                                          50. Haplotypes
                                          51. Ancestry
                                          52. Ethical and social issues surrounding personal genomics
                                          53. Not-so-personal genomics
                                          54. Overview of Module 6
                                          55. Mitosis
                                          56. Sexual life cycles
                                          57. Meiosis, the basics
                                          58. Following genotypes through meiosis, part 1
                                          59. More about meiosis: homolog pairing and crossing-over
                                          60. Following genotypes through meiosis (this time with crossovers)
                                          61. Mating
                                          62. Following alleles through generations
                                          63. Relatedness
                                          64. Sex chromosomes in meiosis
                                          65. Overview of Module 7
                                          66. Genetic analysis began with Mendel
                                          67. Mendels findings and what we now know
                                          68. How to do genetic analysis
                                          69. Mendel's genetic analysis
                                          70. Detecting sex-linkage, predicting outcomes
                                          71. Using crosses to investigate locations of autosomal genes
                                          72. Using pedigrees to investigate family inheritance
                                          73. Using crosses to investigate gene function
                                          74. Genetic analysis: numbers matter
                                          75. Overview of Module 8
                                          76. Heritability
                                          77. GWAS redux
                                          78. Inbreeding
                                          79. Inbreeding in livestock and pets
                                          80. Inbreeding and genetic variation in evolution and conservation
                                          81. Hybrids
                                          82. Plant Breeding & Transgenics
                                          83. Overview of Module 9
                                          84. Polyploidy
                                          85. Aneuploidy
                                          86. Aneuploidy for sex chromosomes
                                          87. Chromosomes rearrangements
                                          88. Consequences of chromosome rearrangements
                                          89. Small changes (structural variation)
                                          90. Junk and selfish DNA
                                          91. Genome evolution
                                          92. Overview of Module 10
                                          93. Origin of Life
                                          94. Mitochondrial genetics
                                          95. Epigenetics
                                          96. Mosaics and chimeras
                                          97. Fetal DNA
                                          98. Genetics of aging

                                          Course Description

                                          This college-level course gives students a thorough understanding of gene function, and enables them to apply this understanding to real-world issues, both personal and societal.


                                          Watch the video: Origin of Life - How Life Started on Earth (August 2022).