Living matter (organics) has cropped up as a subject in several Sections of this Tutorial. Some readers may desire to build up a basic background in Biology. Using the same mini-tutorial approach as was implemented elsewhere in this Tutorial for Geology and Meteorology, and in this Astronomy/Cosmology Section, the writer (NMS) has produced this and the next page. I have relied on one of my most valuable books, Biology, by Peter Raven and George Johnson (McGraw-Hill). In addition, I have drawn heavily on material located on the Internet. Internet tutorial on this subject found by the writer seems to be An Online Biology Book by M.J. Farabee. And here is another Internet site that specifically focuses on paleolife topics: Paleobiology (this site is actually a part of the abovementioned tutorial on Biology, prepared by M.J. Farabee of Estrella Mountain Community College of Avondale, AZ). We also recommend this paperback book: Life Evolving: Molecule, Mind, and Meaning, by Nobel Laureate Christian de Duve, Oxford Press. Two other web sites worth a visit are: (1) a thorough review of almost all aspects of Biology prepared by John Kimball and the more specialized Dolan DNA Learning Center. For a thorough immersion into Earth's early life history, we recommend Andrew Knoll's Life on a Young Planet: The First Three Billion Years of Evolution on Earth, Princeton Univ. Press, Nov. 2003. There is also a helpful Web site that treats developments in the field of Astrobiology (also called Exobiology) hosted by the Astrobiology Branch at Ames Research Center
A proviso:While the main goal of this and the next page is to provide a limited background for the reader on those aspects of Biology that deal with the origin and history of life, the effort will seem sketchy in that many topics that comprise the essence of the subject are treated either cursorily or have of necessity been omitted. The overall treatment of Biology requires considerable time and space (the writer's textbook has more than 900 pages), far more than can be devoted in this Section. But we will examine in some detail the biochemistry of life on this page, a topic of value in reviewing the story of life on Earth on the next page.
The capstone of this Section on Cosmology must surely be a consideration of the most provocative and fascinating Quest in the history of human life: the attempts to determine whether life of any kind - but specifically intelligent life (Pyschozoic is a term created to generalize such a stage of life on exoplanets) - exists elsewhere in the Universe. Philosophically, many on Earth hope that we are unique - thinking beings that are the pinnacle and teleological goal of a Creator's act. Scientifically, most cosmologists, biologists, etc. are coming around to the firm conviction that life does indeed exist elsewhere - throughout the Universe. This is a logical conclusion, since a huge Universe with just one tiny inhabited body on which conscious creatures exist strikes most scientists, and a growing number of philosophers, as extremely unlikely, and, from a practical sense, even a foolish, wasteful action by any Creator (this viewpoint is touched upon again later on this page).
We remind you at the outset of the excellent 2003 book on the subject of life in the Universe, David Grinspoon's Lonely Planets: The Natural Philosophy of Alien Life, cited on page 19-2. A few comments about the history of this idea, extracted from his book, are briefly treated before we begin with the review below:
Grinspoon points out that mankind has been speculating on life beyond the Earth for more than two millenia. The Epicureans of the late period of Greek philosophy before Rome took over that part of the Mediterranean believed that living creatures with intellects lived on one or more of the planets and possibly the stars. Aristotle and Plato, however, argued against multiple worlds. Some early Christian theologians developed ideas that allowed for thinking life within the observed Cosmos (not quite a Universe as we know it today, but a realm that perhaps extended beyond the "spheres" that contained the Moon and Planets; see page 19-2). Similar speculations affected the medieval thinkers. But until Renaissance times, the vast majority held life to be unique to Earth. Copernicus, Kepler, and Galileo gave thought to the possibility of life elsewhere but never did seriously conjecture on the possiblities. Although not well-known to the public and even many scientists, the Italian Giordano Bruno (a Dominican friar fried at the stake by the Church for his radical beliefs) by 1600 had conceptualized a Cosmos filled with multiple Suns and their planets on which life was widespread.
At the dawn of the Age of Enlightenment, a treatise advocating a "plurality of worlds" was published in 1686 by Bernard le Bovier de Fontenelle. This work had a strong influence on thinkers of the day. In the first half of the 18th Century several similar and provocative books by European natural theologians followed. The German philosopher Immanuel Kant was much influenced by these writings and came up with a precursor to modern ideas for the formation of the Solar System. He espoused a much wider distribution of life within our Solar System and probably elsewhere. Laplace, who modified Kant's models, also took the view that life was established beyond Earth. The 19th Century saw similar and varied views favoring the "universality" of life. In the early 20th Century, Percival Lowell popularized this notion with his claims that "canals" existed on Mars. As the dawn of the Space Age arrived in the 1950s, many scientists and much of the general public retained the view that life was likely to be found in other parts of our solar System. The first spacecraft to fly by, orbit, and land on Mars tended to dampen this enthusiasm. But flying saucers and movies about ET and Close Encounters have pumped up the hopes of the Common Man that in time life will be found beyond the Earth.
From an anthropocentric outlook, the importance in understanding planetary formation mechanisms and history is the assumption (not yet a clearcut fact) that planets possessing certain appropriate conditions are the harbors of life. Life, it is believed by Earth dwellers who can think, may well be the most complex and advanced feature in the Universe, based on the presumption that it has evolved into a state resulting in lifeforms that perceive beyond sensing, analyze through reason, and evaluate most other aspects of known existence. Life, under this viewpoint, is the quintessential achievement in the evolution of the Universe to date. Whether life on Earth stands at the pinnacle, or somewhere below, has yet to be established - statistically, it is most likely that somewhere in the Universe even more highly developed living creatures, with superior intellects, exist today or have in the past. (The ideas just enunciated are closely associated with the modern doctrine called humanism).
The expectation that some life exists elsewhere in the Universe will depend on the nature of and conditions for life itself. Life can be defined by properties that are both chemical and functional. Paul Davies, in his excellent book Other Worlds, cites seven essential prerequisites for life to originate, survive, and flourish:
1. There must be an adequate supply of the elements that comprise organic matter - Carbon, Oxygen, Hydrogen, Phosphorus, Sulphur, Calcium, and other elements.
2. There must be little or no risk of contamination by poisonous chemicals (mainly in the atmosphere and oceans), such as ammonia or methane.
3. The climatic temperature must remain within the narrow range of 5 to 40 degrees Centigrade, which is a mere 2% of the temperature range found within the Solar System as a whole.
4. A stable supply of available energy must power living matter; for Earth this is primarily the Sun; internal heat sources, such as the "smokers" vents on the seafloor may also have been involved.
5. Gravity must be strong enough to keep the atmosphere from escaping into space, but it must be weak enough to enable life to move freely within the surficial envIronment.
6. A protective screen must exist to filter out the Sun's harmful Ultraviolet rays, which for Earth is the delicate layer of ozone in the upper atmosphere.
7. A magnetic field must exist in order to prevent cosmic subatomic particles that can damage or kill life from impinging on the Earth.
Missing from the Davies list, but crucial, is the presence of water (whether this is a universal condition or just applies to Earth is not yet established). Water is one of the most versatile and essential substances known on Earth and in and on most planets (both those of the Solar System and around other stars). Water is in essence an Oxygen atom with two embedded protons (from the Hydrogen). Here is a structural representation:
In this configuration the H2O acts as a polar molecule, with one end being positively charged and the other negatively charged. In this sense, water acts both as an acid and a base (but with its pH of 7, it is considered neutral). Water can perform many functions, providing itself as a molecule or as a source of H and O ions. Among functions named as terms are its role as a solvent (breaks down the chemical structures of other substances - especially those held together by ionic bonds), hydrolysis (water splits into H+ and OH-, which react with various substances, especially organic molecules), hydration (water incorporated without change into the crystal structure of a substance), and redox (reduction; oxidation) reactions. Water is the most abundant molecule at the Earth's surface. It is known to humans in its three states or phases: solid (ice), liquid (water), and gas (steam). Water makes up about 70% (by weight) of the human body.
Judging on what we know conclusively from the one sample available to earthlings - namely, life on Earth itself as the only confirmed example in the Solar System - the essential chemical incredients are Carbon, the crucial element in organic molecules (of which proteins are the fundamental component) of great complexity and variety that are the basis of life, together with Hydrogen, Oxygen (some of which is combined as water which dominates the soft parts of human and many other organisms), Nitrogen, Phosphorus, Calcium (mainly in hard parts) and Sulphur, and to a lesser degree other elements as important functionaries, such as Iron, Magnesium, Chromium, etc. The amazing thing about this assemblage of critical elements is that they all at times in the past resided in stars and much of the Hydrogen itself can be traced back to the first minute of the Big Bang. You and I, as humans, are truly star people - our heritage is cosmic in that our ingredients are either primordial- or stellar-derived.
As a quick synopsis on the nature of life, here is a simple list of the "The Characteristics (Properties) of Life", adapted from one put online by the Department of Zoology, Oklahoma State University.
*Organized structures: composed of heterogenous chemicals - in units of "cells"
*Metabolism: chemical transformations that either break down molecules to release energy (catabolism) or use energy to build up molecules (anabolism)
*Homeostasis: which maintains internal conditions separated from an outside environment
*Growth and Development: conversion of materials from the envIronment into components of organism
*Regulation: coordination of the organism's internal functions, including transportation of materials needed to function
*Sensitivity: reaction to select stimuli, physiologically and/or behaviorally
*Reproduction: making copies of individuals via the mechanism of genetic transfer: sections of DNA molecules that contain instructions for organization and metabolism
*Evolution: change in characteristics of individuals, resulting from mutation and natural selection - these result in adaptations; Heredity is the outcome.
Thus, the principal functional manifestations of life (based on our studies of this phenomenon on Earth - our only sample so far) are, to reiterate what was listed above: cellular-organization; reproducibility; growth cycle and dependence on nutrition; metabolism (in higher forms) respiration (in some types); (usually) movement of some kind; propensity to evolutionary modification, and, for vegetative types, utilization of photosynthesis. Intelligent life, furthermore, is marked by consciousness, reasoning, abstraction, reliance on memory, communication, and awareness of time and other essentials of existence; free will and "soul" are properties of a more metaphysical nature and harder to prove as realities.
This next diagram was taken from the Internet without any indication of its source nor any explanation of its content. It is put here without any comment, treating it as a "talking point" relating to some of the questions that are relevant to the nature and origin of life on Earth. The implications within the diagram should also pertain to life elsewhere in the Universe. Draw your own ideas and conclusions.
Life falls into two broad categories: prokaryotic (no cell nucleus) and eukaryotic (nucleus). Life also can be categorized as single celled or multicelled and as autotrophic (obtains nutrients from inorganic sources) or heterotrophic (nutrients obtained by "feeding" on other organic sources). Life is classified by a taxonomic system (first espoused by Linnaeus) of hierarchical catetories - from the highest level (broadest number of constituents) to the lowest (most limited or particular). This ranges through Kingdom; Phylum; Class; Order; Family; Genus; Species; (Subspecies). As an example, consider a honey bee: its species name is mellifera, its genus is Apis, it belongs to te Family Apidae, which is part of the order Hymenoptera, a nenber if the Class Insecta, that falls within the Phylum Arthropoda, in the Kingdom Animalia. Various proposed subdivisions of life at the Kingdom level are used: a common one is the six-kingdom system proposed by Woese: Eubacteria; Archaebacteria (some use Archaea) - both being largely single celled organisms; Protista (eukaryotic; both uni- and multi- cellular), which include algae, foraminifera, radiolaria, and diatoms; (the next three are all eukaryotic and multicellular) Fungi (yeasts; mushrooms); Plantae, with nonvascular plants (mosses et al) and vascular plants (ferns, conifers, angiosperms [flowering plants]); and Animalia,, with 14 phyla, to us the most important of which is Chordata, that includes amphibians, fish, reptiles, birds, and mammals. The evolutionary "Tree of Life" has followed this generalized pattern (alternate schemes have been proposed):
Life is often classified in three broad groupings. Here is such a version of this Tree of Life, with yellow denoting Bacteria, green assigned to Archaea, and blue representing the Eukarya, is (this type of plot of evolutionary trends is known as a cladistic diagram):
This is probably a good place on this page to present an overview about cells. For a fuller treatment go to the Wikipedia web site on Cell
Two fundamental cell types exist: Prokaryotic (no nucleus) and Eukaryotic (nucleus). Both single-celled and multi-celled organisms exist among each type. Both types contain DNA and ribosomes. Prokaryotic cells typically are 1 to 10µm in size; Eukaryotic cells can be 100 µm wide; larger cells are known. This figure depicts the two cell types:
A Eukaryote cell is much more complex, as suggested by this generalized diagram showing its makeup:
Each of these components (most are lumped under the term "organelles") will be concisely defined:
The Cell Wall (called Cell Membrane in animals), in bacteria is usually made of peptilogycan and in eukaryotes cellulose or chitin. Its functions are to enclose the cell interior, protect the cell, and aid in transfer of material in and out.
The Nucleus, commonly spherical and enclosed by a double membrane, contains the chromosomes (gene assemblages of DNA).
The Nucleolus is host to genes for rRNA synthesis.
Cytoplasmis the jelly-like matrix that surrounds the nucleus of a cell and is bounded by the cell membrane. It includes the organelles of the cell as well as the sugars, amino acids, and proteins that the cell uses for growth and reproduction.
Ribosomes are protein-RNA complexes that are sites of protein synthesis.
Vacuoles are open sacs available for digestion or storage of waste products; may contain degraded protein, can become water-filled.
Gogli Apparatus consists of stacks of vesicles (openings) in which proteins made in the cell are prepared for export from the cell
Lysosomes are vesicles, derived from Gogli A., containing digestive enzymes that attack defunct organelles and other cell debris.
Centrioles are specialized organelles that produce microtubules that influence cell shape, move chromosomes during division, and aid in developing cilia and flagella.
Peroxisome use enzymes to remove superfluous electrons and Hydrogen atoms; Hydrogen peroxide is a by-product.
Mitochondria are double-membrane organelles that provide "power" from the cell by oxidative metabolism.
Endoplasmic Reticulum serve as networked membranes that aid in making vesibles; also assist in synthesizing proteins and lipids.
Not shown in diagram: Chloroplasts, which control photosynthesis in plants and Chromosomes, which are long DNA threads that host hereditary information.
These definitions refer repeatedly to DNA and RNA. These are two nucleic acids which will be discussed in detail further down this page.
Understanding how life is organized into cells (through the science of Biology) requires some core knowledge of Organic Chemistry and its subfield Biochemistry. Only the most rudimentary ideas can be covered on the relevant sections of this page. Most of the illustrations were taken from the Online Biology Book, cited above, prepared by M.J. Farabee. He attributes on his site most of the illustrations we will use to Purves et al.; Life: The Science of Biology; Sinauer and Assoc. Publishers and M. Freeman & Company.
Organic substances are combinations of Carbon with other elements (most common are Hydrogen, Oxygen, Nitrogen, Sulphur, and Phosphorus). Bonding with the Carbon is of the covalent type - two atoms share one or more valence electrons. There are literally tens of thousands of organic compounds. But most of these can be grouped in systematic ways. One is the so-called functional group in which there is a basic unit built around carbon that can be combined with other elements or radicals. This diagram gives some examples as an overview (other, more specific diagrams will appear later on this page):
Organic molecules in their simplest form constitute the Hydrocarbons which are built from Carbon atoms (which have 4 electrons in their outer shell and can accept 4 more to complete the shell. This can start from the simplest Hydrocarbon (CH4, methane, and built up in chains or rings, as indicated in the diagrams below:
A wide range of more complex organic molecules can develop from adding various molecular functional groups that include N, O, P, S and other elements to open positions in the Carbon shell or to Hydrogens. These are the principal units:
These molecular varieties fall into groups such as saturated Hydrocarbons with single H-C bonds (Alkanes), double bonds (Alkenes), and triple bonds (Alyknes); ring structures are represented by Aromatic Hydrocarbons. Isomers are organic molecules with the same chemical formula but different atomic arrangements. Among the derivative organic molecules (Hydrocarbons with parts replaced by functional groups) are Alchohols (--OH functional group), Ether (--O--), Aldehyde (--CHO), Ketone (--CO--), and Carboxylic Acid (--CO3H).
Biochemistry is a vast subfield of the more general Organic Chemistry. While the subject is complex and detailed (see links above), a few general ideas developed around key illustrations taken from M.J. Farabee's site (cited above), and one from Raven/Johnson are introduced here:
There are four major groups of organic molecules that also are the fundamental categories in living matter: Lipids; Carbohydrates; Proteins; Nucleic Acids (RNA; DNA). We will describe the first two in limited detail.
Lipids include fats, fatty acids, certain oils, waxes, terpenes, and steroids (one example being cholesterol). They consist of polymers of CH2 and CH3. Glycerol, a typical fatty acid, has the formula: HOCH2CH(OH)CH2OH. Palmitic Acid has this structural arrangement:
The molecular structures of some common steroids are depicted below:
The second major group, the Carbohydrates, also known as Saccharides, includes sugars, starches, glycogens, and cellulose. The basic formulaic unit is: CH2O. One important group, the Monosaccharides, includes ribose and deoxyribose, ring structures made up of pentagonal (5 Carbon) sites - these are two fundamental components of RNA and DNA. Example:
Glucose is said to be the most abundant biochemical molecule within terrestrial life: Its formula is C6H12O6. Here are several views of glucose; at the top are two isomers, below is a 3-D stick and ball representation, and at the bottom is a side view:
Structures comprised of two joined rings are Dissarcharides (e.g. Sucrose and Lactose). Chains of rings make up Polysaccharides" These include starches (which store food energy in plants), glycogen (energy storage in animals) and cellusose (important cell wall component in plants). A starch molecule and
Proteins, the most abundant constituents of organic matter, are built from linked individual amino acids. There are 100s of such acids but only 20 occur in proteins involving human tissue. The basic protein unit consists of a central Carbon, an amino group, a carboxyl group, and a side group, labeled R, that can consist of a variety of functional groups; the general molecule looks like this:
Three examples of individual amino acid types are shown below:
The 20 amino acids are shown structurally in terms of different side groups in this chart:
All 20 are α-amino acids, meaning that the amino group is always bounded to a Carbon atom. Various combinations of the 20 can link (bond) with one another (amino group to carboxyl group) to form polymers. The linkage is termed peptide bonding. Oligopeptides link only a few amino acids; chains of 100s of amino acids (polypeptides) are common:
Protein synthesis is a major goal in biochemistry. This is proving difficult because getting the amino acids in the right order is hard, unwanted reactions among side chains is common, and peptidization gives off energy which can decompose the desired end product. Protein structure can be simple chains (primary) or helical or pleated (secondary) or complexly folded (tertiary and quaternary structures).