www.UsHumans.net: Chapter 5



 

 

 

Part Two


The nature of a human


 



Chapter 5


The nature of the molecules of life, and the sequence of plants and animals that have developed on the Earth


In the first part of this chapter we will see how the electrical force holds together combinations of atoms and that the molecules of life consist of large numbers of these naturally occurring combinations. (Molecules are combinations of two or more atoms bound together.) This means that the fundamental basis of life is nothing but the electrical interactions of atoms. (This interaction was described in Chapter 2.) The second half of this chapter contains a summary of the sequence of animal types, from bacteria to mammals, that have developed on the earth.

    We will see that a certain molecule, called DNA, consists of a pair of parallel strings of atoms. These paired strings are bound together such that each is a sort of mirror image of the other. When the pair becomes split apart, each of the two strings will gather components from the surrounding chemical mix to rebuild its missing mirror-image half. The result of this splitting and rebuilding is that the original pair of strings has been replaced by two pairs of strings. This is a self-duplicating molecule. This molecule also electrically guides the sequences of gathering-up of smaller molecules into larger combinations that grow and operate an individual plant or animal. DNA grows an individual from ingested and absorbed chemicals altered in the right way to produce the chemicals forming various tissues and organs; DNA also chemically directs the operation of an individual through the production of those chemicals needed at any moment. These are the things that DNA does naturally. Change DNA and the resulting individual will change.

    It is natural that any change in the resulting organism that makes it better matched to its surrounding environment of climate, predators, and food will also make it more likely to live long enough to produce additional generations. Any organism poorly matched to its surrounding environment will not as likely be around long enough to produce an additional generation. Keep in mind that when two different species seek the same food and share the same environment, the species having just a 1% better match to the environment will increase in number sufficiently faster to swamp the other within a couple dozen generations. The surrounding environment selects those individuals possessing the best-matched characteristics and unselects those that are unmatched. An individual is “selected” simply by being well enough matched to its environment to live long enough to produce offspring. As the environment of climate, predators, and food changes, so too will the DNA that best matches that environment. A range in DNA always exists in the current members of a species. That collection of individuals have a range in characteristics due to a range in their DNA. Just as the height of people follows a bell-shaped distribution, so too will their abilities to handle cold, digest peanuts, and so on. (For more about bell-shaped curves, visit www.upscale.utoronto.ca/PVB/Harrison/ErrorAnalysis/BellShaped.html or http://math.elon.edu/statistics112/norm_dist.html.) A species is more likely to survive a change in its environment if its individuals possess a sufficient range in characteristics that some individuals are already suited for that changed environment; they already possess DNA better-matching the changed environment. As the environment changes in time, the peak in the bell-shaped curve of an important characteristic shifts. The sequence of changes in the individuals of a species is described as evolution and it occurs through natural selection by the environment of climate, predators, and food. Changes occur through the generations. Generations last but a few minutes in bacteria and a few days in insects. Visit http://devolab.cse.msu.edu for information about a project in which digital organisms evolve at the speed exercised by computer software.

    This following description of the origin of the molecules of life is a summary of The Realm of Molecules, by Raymond Daudel. The primary source for the description of the chemistry of our bodies is The Chemistry of Life by Martin Olomucki. The outline of the sequence of the species of life on Earth was taken from Life Through Time, by Harold L Levin. (Technically, two animals are said to be of the same species if the two can mate and produce offspring that in turn are also able to produce offspring of their own.) An on-line, talking glossary (with illustrations) of biological terms has been developed by the Human Genome Project and can be found at www.genome.gov/page.cfm?pageID=10002096.


Electrical binding in atoms is the physical basis of the molecules of life


The electrical interaction is one of the five basic forces found to exist in nature, as described in Chapter 2. We have seen that about one hundred types of atoms occur in nature, including hydrogen, helium, carbon, and oxygen and such and that nearby atoms interact through the electrical force involving their outermost electrons. Living creatures consist of one to one-trillion cells, each of which contains one trillion interacting atoms. The operation of each creature occurs through thousands to millions of chemical reactions, each of which involves the electrical forces among the charges of the mixing atoms. The electrical interaction forms the underlying, physical basis of the multi-atom molecules of biology and life.

    In chemical combinations, atoms become mutually bound to each other through either the lending or sharing of outer electrons that occurs between pairs of nearby atoms (see The Sciences, An Integrated Approach, by James Trefil and Robert M. Hazen). As one atoms lends an electron to another, the giving atom is left with a net positive charge while the receiving atom acquires a net negative charge; these two oppositely charged atoms then experience a mutual, electrical attraction in a so-called ionic bond. An electron can also be shared among many atoms within a molecule (covalent bond). Most atoms have only one or two electrons that are shareable, but carbon has four. Since each carbon atom can bond with up to four neighboring atoms, it is able to forms rings, chains, and branching structures not possible for other atoms. The building blocks of living structures consist of these carbon structures. Electrons are shared by many atoms in metals (metallic bond). This relatively free movement of electrons is responsible for the shine and for the rapid heat transfer of metals. In some molecules, a shared electron spends more of its time orbiting one of the partnering atoms. In affect, this causes the side on which it is spending the most time to be more negatively charged than the less-often visited side. These are referred to as polar molecules. Hydrogen can be polarized in this way and become bound to other atoms–especially oxygen and nitrogen–in a relatively weakly bond (hydrogen bond). In Chapter 2 we saw that a block of atoms that contains equal mixtures of positive and negative charge and so is electrically neutral can still be attracted to a nearby, external charge. This so-called van der Walls force can form a weak bond between molecules.

    Molecules react with other atoms and molecules, sometimes merging, sometimes breaking apart, and sometimes forming new collections out of the interacting units. The ease with which two approaching molecules can electrically interact depends on their shapes and charge distributions and also on their relative orientations and speeds while near each other. Each type of molecule has a specific shape and consists of a specific combination of atoms and, perhaps, smaller molecules. Biological molecules contain thousands to millions of atoms and have convoluted shapes. Their outer surfaces have numerous bumps, indentations, and projections. Some of these features or regions have an overall positive electrical charge, others have a net negative charge, and yet others are neutral. Two large collections of atoms can become bound either by sharing electrons between adjacent atoms or molecules or through the mutual attraction of oppositely charged regions of their outer surfaces.

    To picture a convoluted shape you might imagine gluing soccer balls together. You might first glue twenty soccer balls into a roughly spherical clump. Then form an arch using another thirty soccer balls and attach it onto the first clump such that the arch sweeps out from the left side and rejoins on the right. Then add more arcs, and bridges between arcs. The shape of a molecule can become ever more tangled as its number of atoms increases. They take on strange shapes because some areas of a molecule can have an overall positive electrical charge while other portions of the same molecule have an overall negative charge.

    As you attempt to join two molecules into a larger conglomeration, the two pieces are able to fit together only if and where two constituent molecules can share electrons or if they are facing each other such that a negatively charged portion of one attracts a positively charged portion of the other. Often, there is no relative orientation in which the pieces attract each other. You might imagine what would happen if you similarly attempt to join two handfuls of magnets. Depending on their orientations, some might fly away while others join. If two different types of molecules drift past each other while having oppositely charged regions facing one another then these two molecules can join to form a yet larger molecule; two molecules do not merge when like-charged regions face one another because of their mutually repulsive electrical force. Those molecules that can merge, will; in fact, they must. Those that cannot merge will not do so. If many different types of atoms are mixed together then those that can do so will merge with others to form molecules. (Sometimes the presence of a certain chemical, a so-called catalyst, will cause others to interact more rapidly.)

    The one hundred types of atoms found in nature can be placed side by side two at a time, three at a time, and so on, into countless sequences of increasing numbers of atoms. But few types of atoms simply placed next to each other will be able to electrically hold on to each other. Of the zillions of possible combinations, most do not produce an electrically stable molecule and so do not occur in nature. (In the last century or two, chemists have found many rules that help to predict which combinations can form stable molecules.) Any combination that is stable will occur whenever its components are mixed together.

    Out of the one hundred types of atoms, we have seen that carbon atoms are the most suited to be joined together into rings and long chains containing hundreds or thousands of atoms. Much of biology involves the organic chemistry of carbon. For example, proteins are large molecules formed by combining several types of atoms and lots of carbon rings. The largest biological molecules contain billions of atoms. Often, these organic structures are more stable than many of the inorganic molecules because they are not as easily torn apart. Organic chemicals have been found in space and even on Halley's comet. All of the Earth's life-forms consist of these organic compounds.

    Four families of organic compounds form the building blocks of life: twenty amino acids, carbohydrates such as sugar and glucose, lipids or fatty acids that do not dissolve in water and so form cell walls (see www.life.uiuc.edu/crofts/bioph354/membrane_phase.html) and store energy within fat, and the five nucleotides that comprise DNA and RNA (visit www.sis.nlm.nih.gov/enviro/toxtutor/Tox3/a25.htm for more information about these components). The molecules of each of these four organic compounds consist of about twenty carbon, oxygen, nitrogen, and hydrogen atoms (97.5% of the atoms within our bodies consist of these four elements, while calcium comprises 2%, phosphorus 0.2%, sulfur 0.1%, and all others 0.2%). Though hundreds of amino acids have been synthesized in the lab, only twenty different amino acids appear in living systems. These four types of compounds form the building blocks of larger structures– just as a home is built of individual bricks, doors, and windows (see Trefil and Hazen)–in that our bodies consist of, and operate using these four things. In particular, the twenty amino acids form the proteins used in the operation of our bodies.

    Strings of twenty or so amino acids create the simplest proteins containing about four hundred atoms. Many proteins contain hundreds to thousands of amino acids joined into a long chain that folds over and electrically attaches to itself in several places, producing a convoluted, three-dimensional structure. To illustrate this convoluted shape, consider that a rubber band consists of molecules formed into a strip. While it usually forms a ring, we could cut it and lay it flat on a table. This strip could be laid down left to right for a short distance, folded back on itself, and laid down right to left in an adjacent strip. This could be repeated many times to have an s-shaped sheet. We could next place our palm on top of the sheet and rub forward to cause the sheet to clump–as rubber bands do–into a three-dimensional structure. We might take three other rubber bands and repeat this procedure to have four clumped structures of s-shaped sheets of rubber band strips of molecules, and then place the four next to each other, two above the other two. The U.S. National Library of Medicine has a three-dimensional illustration of the similarly-shaped Phenylalanine hydroxylase enzyme at http://ghr.nlm.nih.gov/ghr/picture/ph. The results of a computer model of the protein folding process is shown in the video at http://www-vis.lbl.gov/Vignettes/RAOliva/t209/movies/71150_50.mpg. Each protein has a specific shape, formed from clumped sheets of s-shaped strips of amino acids. Each protein simultaneously has one-, two-, and three-dimensional shapes (they have a fractal dimension). The shape of each protein determines its chemical properties in that it will electrically hold onto those other molecules having a compatible shape.

    Some examples of protein include hair, nails, silk spider webs, tendons, and connective tissue but proteins serve many important functions in the body. A hormone is a protein that gives molecular messages to organs. For example, hemoglobin is a protein that transports oxygen from lungs to cells. Proteins determine which chemicals can flow into or out of cells. Proteins play a crucial role functioning as enzymes.

    Enzymes are a class of proteins that speed up (catalyze) reactions between specific substances. To see how enzymes work, consider that the shape of a grocery store egg carton is such that it holds a dozen eggs in individual little pockets. Each egg is held close to others. Imagine that the egg carton was able to crack together two neighboring eggs and cook them into a flat oval. Since the shape of the two cooked eggs has changed, the egg carton will no longer hold them in place. The two eggs can now easily slide out of the carton. The carton has not changed but the shape of the two combined eggs have. Enzymes perform a similar function in that they have the right “carton-shape” to hold two smaller molecules together long enough for them to merge into a new molecule that no longer fits in the carton and so moves away. The enzyme has not changed but the shape of the two held together molecules has changed. The enzyme helps along the chemical reaction that merges and changes other molecules. Our bodies vary the number of enzyming proteins to vary the rate of chemical reactions, thus controlling specific functions. In the next section, we will see how DNA controls the production of reaction-controlling proteins (enzymes).

    The four so-called nucleotide molecules adenine, thymine, cytosine, and guanine–which we'll call A, T, C and G molecules–have important properties when placed together to form lines of molecules. (The fifth nucleotide is uracil, symbol U, which replaces thymine in the formation of RNA.) When these four types of molecules face each other, their size, shape, and charge distribution enables just certain pairs to be able to hold electrically onto each other. It occurs that A and T molecules will hold electrically onto each other, but they cannot hold onto any C or G molecules; similarly, C and G molecules will hold onto each other but cannot hold onto either A or T molecules.


DNA naturally duplicates itself


DNA is a long string of thousands to millions of the four nucleotides A, T, C, and G. DNA molecules contain billions of atoms and are a few centimeters (an inch) in length but only a few molecules wide, as explained in Our Molecular Nature by David S. Goodsell. The structure of the DNA molecule was determined from x-ray analysis (see The Double Helix edited by Gunther S. Stent). DNA molecules resemble a ladder in that they take the shape of two parallel atom-strings laid side by side but twisted into a helix as the “ladder” moves upwards. The “ladder poles” consist of a sugar phosphate, while the “ladder rungs” consist of either a G-C or an A-T pair. The left and right halves of a ladder rung each consist of one A, T, C, or G molecule. Whenever the left half of a ladder rung consists of an A molecule, the right-side of that rung must have a T molecule, similarly for C and G molecules. The U.S. National Library of Medicine has an illustration of DNA at http://ghr.nlm.nih.gov/ghr/picture/dna. Tufts University has an animated video clip of a DNA molecule at www.tufts.edu/as/wright_center/cosmic_evolution/docs/fr_1/fr_1_mov.html.

    The two parallel ladder poles are separable. (The production and presence of a certain chemical causes the ladder to sort of unzip.) As the ladder poles separate, each of the rungs also become divided into two, separating the A-T and C-G pairings. Each ladder pole then has its set of ladder rung halves stick outward into the surrounding chemical soup that includes freely drifting A, T, C, and G molecules. Each of the A-molecules of a ladder rung half can electrically re-attract only another T molecule because that is its "mirror-image," similarly for C and G molecules. In this way, the right side of the ladder can gather up a replacement of its missing left side by electrically attracting another set of mirror-image molecules. The two separated molecule-strings have attracted another set of molecules, one-by-one, out of the surrounding chemical mix within the cell to gather its "mirror-image." The result is that the DNA molecule has reproduced itself (more technically, it has replicated itself). It took a number of groups of twenty carbon atoms before a self-duplicating arrangement formed. Those molecules that naturally duplicate themselves, do; in fact, they must.

    The fact that DNA is naturally self-duplicating is demonstrated by placing one DNA molecule into a soup of A, T, C, and G molecules. Heating the soup causes DNA to separate into its two strands. When the soup is then cooled, the two separated strands will each rebuild their mirror image, resulting in two complete DNA molecules. Repeat this cycle of heating and cooling many times. Each time the soup is heated and then cooled the number of DNA molecules will double. After ten such cycles, the amount will have doubled ten times, which is a one thousand fold multiplication. In this way a large amount of DNA can be obtained from a small sample, as is done in scientific studies and in crime labs.

    Errors often occur during duplication but they are usually found and removed because they cause a local bulge or kink in the inaccurate copy, as described by Trefil and Hazen. For example, two successive G nucleotides on one ladder pole sometimes attach to a single C nucleotide on the opposite ladder pole. A bulge results just as would occur if, during construction of a ladder, you accidentally nailed two ladder rungs from the left pole to the same spot on the right pole. The resulting bulge is found by an enzyme that wraps itself around DNA and reacts to any bulge simply by cutting away that section of one ladder pole. The next time the DNA is duplicated, the missing section is automatically re-created. Repairs are continually made to correct damage caused by any other source, including ultraviolet light, x-rays, and countless types of eaten or absorbed chemicals.

    DNA is also changed or damaged by radiation. Radiation damage to people, or any other animal, occurs when energetic light-waves (gamma radiation) collide with their DNA molecules. These energetic light-waves are stronger than the usual medical x-rays. Damage is also done as electrically charged radiation, which consists either of positively charged helium nuclei (alpha radiation) or negatively charged electrons (beta radiation), pulls electrons away from the atom's of your body. A tiny change in a DNA molecule can have a large affect on the operation of an individual. Around the year 1900, the effects of radiation began to be learned the hard way by the physicists who first studied its properties, as mentioned in Chapter 2. In fact, Marie Curie’s lab book contains radioactive fingerprints. (In 1911, Marie and her husband Pierre won the Nobel prize in chemistry for their research on radioactive atoms. Marie later won the Nobel prize in physics. In 1935, their daughter Irene and her husband Frederic Joliot-Curie won the Nobel prize.)

    During the early years of the Earth, 4.5 billion years ago, no DNA molecules existed. From the start, molecules were forming into those larger and larger structures that could naturally form. Once formed, molecules remain intact until they become sufficiently heated or until either broken down or further enlarged through encounters with other chemicals. For the first billion years of the Earth's history, these molecular structures grew in length at an average rate of about one atom per year. (The Tufts University animation at ww.tufts.edu/as/wright_center/cosmic_evolution/docs/fr_1/fr_1_mov.html shows the origins of life on Earth.)

    In time, a molecular structure became self-duplicating. Once a self-duplicating molecule had developed from the chemical mix, it would naturally occur that any change making that molecule better able to make duplicates would result in increased numbers of that molecule. Each successive generation in this molecule could give rise to slightly changed copies. Those changes that resulted in less stable duplicates could mean an end to that version of the molecule. Evolution began with the first self-duplicating molecule. Your own DNA, and that of every other species on the earth, is a direct descendent of the first self-duplicating molecule that developed nearly 4.5 billion years ago.


Cells, tissues, and organs


By three billion years ago, DNA and its surrounding pool of A, T, C, and G molecules came to protect itself from chemical bombardment by becoming enveloped within an enclosure. The resulting, so-called cell is the fundamental unit of life in that all living matter–from bacteria to plants and whales–is composed of cells and that every cell arises from previous cells. (This was first proposed by Theodor Schwann in 1839, see Trefil and Hazen). Every living organism consists of cells that contain DNA. The size of a cell usually ranges from 0.01 to 0.1 millimeters (0.004 to 0.04 inches), but in a larger example, a bird egg is also a single cell. Each human contains one billion cells per gram. An entire person contains a few trillion cells. Each cell contains a few trillion atoms (a trillion is a million-million) and its own copy of DNA arranged into twenty-three paired pieces called chromosomes.

    Cells were first observed in a microscope by Robert Hook in the year 1663. By 1675, Anton van Leeuwenhock had observed several types of cells and noted that water contains many microscopic, living creatures. (One never forgets the first time one sees amoebas and such in a microscope, the rings of Saturn in a telescope, or lightning bolts emitted from a Tesla coil. These are three of the most impressive sights for the beginning nature lover.) Hundreds of species of microscopic creatures can be seen at the website http://microscope.mbl.edu/baypaul/microscope/general/page_01.htm. The Exploratorium has video clips of amoebas and such at www.exploratorium.com/imaging_station/gallery.php. You might also visit www.microscopyu.com/moviegallery. Visit www.genome.gov/Pages/EducationKit/download.html for an animated time-line of biological discoveries and to download Milestones in Genetics: Timeline from the Human Genome Project website.

    In the variety of organisms today, cells exist in about two hundred shapes and sizes, and they have taken on various specialties. For example, nerve cells allow the flow of electrical charge while muscle cells are stretchable. The structure of a cell can be seen at the National Library of Medicine website at www.sis.nlm.nih.gov/enviro/toxtutor/Tox3/a24.htm. Living creatures consist of a hierarchy of components: chemicals form cells that comprise tissues that in turn make organ systems. Organs include the liver, heart, kidneys, and brain and such. For 3-D animations and internal views of organs taken with cameras, see www.medicdirect.co.uk/virtual_body/default.ihtml. The human body consists of eleven organ systems (see www.sis.nlm.nih.gov/enviro/toxtutor/Tox3/a22.htm) including the circulatory, nervous, muscular, skeletal, reproductive (which comes in two varieties), urinary, digestive, respiratory, lymphatic, cardiovascular, and endocrine systems. (To see the beginnings of surgery simulators, which are similar to flight simulators, for use in medical school, visit http://virtual.uta.edu/CD/SYH%20Research/demopage.htm.)

    Each organ within our body contains cells organized into four types of tissue: epithelial, connective, nerve, and muscle. These tissues are shown at www.sis.nlm.nih.gov/enviro/toxtutor/Tox3/a23.htm. Epithelial tissue forms the lining around organs and also forms skin. Connective tissue includes ligaments, tendons, cartilage, bone, blood, and the fibers of organ walls. This tissue connects, supports, and protects other tissues. Nerve tissue forms brains, transmits signals to muscles, and senses hot and cold and other exterior conditions. Muscle tissue includes the four varieties that continually move and support bodies, flex when signaled to move particular bones, continually beat hearts, and the smooth variety that contracts on its own to move the internal fluids of bladders, lung bronchi, and the walls of the blood vessels. Blood and nerve signals flowing within every organ. From head to toe and backbone to skin, we have a couple dozen organs, a couple hundred bones, and about five hundred body components, including muscles and cavities and such. The Visible Human Project at www.nlm.nih.gov/research/visible/visible_gallery.html has a video clip showing a succession of slices through a person, from head to toe. There is little difference in cell, tissue, and organ components between us human beings and any other mammal, and even less difference between us and any of our fellow primates. There are increasing numbers of differences between us and reptiles, amphibians, fish, insects, worms, and plants.


DNA naturally builds and operates entire individuals


DNA also contains the chemical-construction maps used to produce the chemicals or proteins needed to operate an individual. Every aspect of the operation of our bodies occurs through a series of chemical reactions. Within each cell, the presence, over-abundance, or under-abundance of any one of a number of specific chemicals, foreign or domestic, will activate the production of a responding or counteracting protein. We maintain internal, chemical equilibrium this way. In the case of a counteraction to a triggering chemical, protein production ceases when the triggering chemical has been actively converted into an ignorable chemical. DNA contains the information needed to produce the proteins in reaction to the triggers. The greater the number of reactions to control and triggers to deal with, the greater the information content of a creature’s DNA.

    In reaction to the triggering chemical, a copy of a specific section of DNA is made within the cell nucleus by temporarily unwinding that section. Such a DNA section is called a gene. One gene contains the chemical-construction map needed to produce one specific protein. This is the so-called Central Dogma of biology. The copy of the DNA-segment or gene is called RNA and is transported to another organelle within the cell, the ribosome, where the chemical-construction map will be followed to mass-produce the specified protein that will serve as the enzyme (chemical catalyst) needed to control that triggering chemical and its reaction rate. DNA “says” when that chemical is present, produce this chemical by forming a series of amino acids and joining them together. The entire process is described as the transcription of DNA into RNA followed by the translation of RNA into proteins. Visit www.genome.gov/Pages/EducationKit/online.htm for an animation.

    Certain diseases are caused by the failure of DNA to produce a specific protein. For example, diabetes occurs when the body does not produce the protein insulin. The newly developing techniques of gene therapy hope to replace specific sections of a patient’s improperly functioning DNA with working copies. This technique has successfully treated severe combined immunodeficiency (SCID). Trefil and Hazen relate that Ashanti de Silva was the first person to have defective genes in blood cells replaced with normal ones.

    How does DNA serve as a protein construction map? We saw that DNA consists of strings of A, T, C, and G molecules or nucleotides. How many combinations of A, T, C, and G molecules can be made in a series of two or three of them? Sixteen different pairs of nucleotides can be made from these four nucleotides because there are four ways to choose the first of the pair and four ways to choose the second, so its 4x4=16. Eight of the sixteen possible pairs are GG, GC, GA, GT and CG, CC, CA, CT (these are not ladder rung pairs but successive rung components). Sixty four combinations can be made that consist of a series of three of these nucleotides (notice that 4x4x4=64). Two examples are AGC and AAT. Recall also that the same twenty amino acids–and no more–are present in every living creature and that each specific protein consists of a specific series and number of amino acids joined together in a structure that is simultaneously one-, two-, and three-dimensional. The DNA construction map indicates the sequence of amino acids that are to be joined by coding each as a series of three A, T, C, and G molecules. For example, Olomucki explains that the triplet sequence A-G-C followed by A-A-T will cause a tyrosine and an alanine molecule to be formed out of the surrounding mix of chemicals and then joined together. (Visit http://en.wikipedia.org/wiki/Genetic_code for the complete, 64-element genetic code.) Triplets of A, T, C, and G molecules could code for sixty four amino acids but only twenty occur within the Earth’s life forms. Three of the extra forty-four are used to indicate the ends of genes. The remaining forty-one extras allow for a redundancy that protects against partially damaged triplets. Chemical disruptions, attacks, and damage occurs many times per day.

    DNA also contains the chemical-construction map used to produce the sequence of chemicals needed to grow an entire individual–from seed to adult–from its food and from absorbed chemicals. An organism ingests (eats) and absorbs chemicals from its surroundings, breaks them down into simpler molecules, and then recombines them into other chemicals determined by the DNA of the organism. A complete plant or animal develops from the single cell of its seed by producing the sequence of molecules indicated by its DNA code–its "construction and operation map." The chemicals within our food are altered to become the chemicals needed to operate and grow ourselves. Feed milk to your newborn infant and his or her DNA will direct the conversion of the chemicals within milk into the chemicals comprising your baby. Place a seed into the ground and its DNA will reform absorbed chemicals into those chemicals that are a plant.

    The flowering rose is a relatively new type of plant (flowers appeared just fifty million years ago). It contains DNA molecules each held together by the electrical forces among its constituent atoms. DNA contains the directs a sequence of reactions that take certain external chemicals and then alter and mix them with internal chemicals to result in those chemicals that are the rose. This chemical series will result when you place the blobs of chemicals of the rose seed into contact with the chemicals of the ground and air. The reactions occur naturally–and are going to occur; indeed, they must. Through its particular series of chemical reactions, a rose will develop from its seed. The chemicals of the seed and of its surroundings, and the chemical directions of the seed's DNA, are going to result in a rose. In the same way that pushing an initial chemical through a container of a second chemical, and the resulting mixture through a set of additional chemicals, always produces the same result. The rose consists of a large number of atoms and molecules and a large number of chemical reactions. The incredibly complicated, molecular nature of the rose increases its beauty tremendously.

    To grow an entire individual from a single cell requires that millions of chemicals be produced in the right order. The information needed to produce this sequence of chemicals is contained in the individual's DNA. That information does not spring into being at the moment of an individual’s birth–nor did your own; it originated in the first self-duplicating molecular structures of the early earth and evolved through four billion years of time, generations, and environmentally tested changes. Through that time, DNA has accumulated an increasing number of chemical-construction instructions and an increasing amount of information. This information accumulated through the generations as DNA changed through the generations. Each change in DNA results in a change in its end product: the growth and operation of an individual.

    DNA contains the chemical-construction map used to produce the sequence of millions of chemical reactions to grow and operate a complete individual. Having millions of reactions means that there are millions of things that can go wrong. Errors can occur because the components are the outcome of a huge number of chemical steps. (The number of errors is minimized, but not eliminated, by the built-in redundancy of the genetically coded directions.) A single error can affect many processes. Nearly always, an error in any of the chemical steps will result in an individual that does not function as well. This individual will then be less likely to live long enough to have children. But every once in a while an error will result in an improved individual. These mutations are responsible for a large part of the evolution of species that occurs as the environment naturally selects better-matching individuals. The chance of an error resulting in an improvement is small, just like the chance of a person winning the lottery, but both do occur.

    In Physics as a Liberal Art, Trefil calculates that the chance of a person in the U.S. dying in an accident during the next hour is about one in ten million. (The calculation involves the number of persons in the U.S., the known number of accidental deaths per year, and the number of hours in a year.) In the next hour, a person is far more likely to die in an accident than win the lottery. What is the chance that a person wins the lottery but dies in an accident before collecting? The combined chance is found by multiplying the two independent chances.

    The biologist Susan “Zen” Buraceski, explains that life forms have five defining characteristics: they separate themselves from their surroundings, exchange chemicals with their surroundings, maintain internal equilibrium, reproduce themselves, and react to their surroundings. It is important for a life form to keep itself and its packet of useful molecules separate from its surroundings; that is the purpose of its enveloping membrane. Internal equilibrium is important. Whenever there is too much or too little of one chemical within a cell, counteracting adjustments are made to cancel the imbalance. We see that DNA is central to each of these defining characteristics. Bacteria were the first collections of molecules that can be considered to be alive. In the continuation of the crucial, reproduction property of the earliest, molecular-sized proto-lifeforms, the first goal of microbial life is to reproduce, which it does every few minutes. (The first ability we had was to reproduce, later we added livers and legs and such.) Bacteria reproduce at a rate of about one thousand generations per year, or one trillion generations per billion years.

    The single-celled E. coli bacteria live in our stomach and help us digest food. Scientists have found that an E. Coli organism contains 500 kinds of small molecules, 3,000 proteins, and 1,000 nucleic acids. There is a constant and ordered sequence of chemical reactions occurring within this "simple" life-form. (For example, you might look at its lac operon process.) Similarly, we multi-celled humans maintain internal chemical equilibrium through the balance of many thousands of interacting chemicals. Each of our cells are protein manufacturing centers. Each type of cell manufactures its own specific proteins by following the appropriate section of DNA. (Each cell contains a complete copy of the animal’s DNA but each cell uses only certain sections of the entire DNA.) The operation of each of our organs involves thousands of interacting chemicals. Within either E. coli or humans, each individual reaction obeys the laws of physics and chemistry and can be reproduced in the laboratory.

    A virus–for example, one that causes influenza–is a short section of DNA enveloped within a protein. A virus is not alive because it does not carry on metabolism and can not reproduce itself. Once a virus gets inside a living cell, the cell begins duplicating the virus as if it were its own section of DNA. The cell dies after it has made a number of copies of the virus. Since a virus is not a bacterium, antibiotics have no affect on them. Dr. J. Craig Ventor, who lead much of the work on the Human Genome Project, recently announced that he has built a virus from scratch. He says the process required but two weeks to carry out. This work not only goes a long way in verifying our understanding of the molecular and genetic basis of living matter, but also represents an important step in fighting disease. In the future, viruses may be designed in the lab that will replace a diseased cell’s damaged DNA with undamaged DNA.

    In review, within DNA each sequential triplet of A, T, C, and G molecules codes for one amino acid, and a varying order and number of amino acids form each protein. One gene codes for one protein. Each human gene typically consists of a series of one thousand A, T, C, and G molecules (or base pairs) mixed along a strip of DNA, see http://ghr.nlm.nih.gov/ghr/picture/gene, but the number varies from a few hundred to a couple million. DNA contains the chemical-construction maps used to produce the chemicals or proteins needed to grow and operate an individual. The collection of proteins coded within a creature’s DNA will grow and operate that creature. In addition, DNA is a self-duplicating molecule that changes through the generations. Those changes making the resulting creature better matched to its environment of climate, predators, and food are more likely to be passed on to future generations simply because future generations then occur. Those not well-matched produce fewer offspring. DNA forms the molecular basis of all of the Earth's life. DNA is a naturally self-duplicating molecule-machine that naturally directs the sequences of chemicals that grow and operate an entire individual. This self-duplicating, self-operating, and self-building combination of molecules is life. This is the nature of life. Life is a molecule-machine.

    DNA results in life. Life seems mysterious if we look only at ourselves, wondering why we are so different from snails, but not so mysterious when we see that we that we are the natural end product of DNA and its four-billion-year accumulation of chemical-construction information. Remember that the earliest biochemical molecules increased in length at the meager rate of about one atom per year. By three billion years ago DNA contained the design code for bacteria, but your DNA has a four-billion-year molecular history. It is the current state of a large molecule altered through generations of duplications. All of our biological understandings are explained in terms of DNA and its natural changes through time. It has been found that both living and nonliving matter are made of atoms and molecules and that both follow the same fundamental rules of nature–that is, one set of rules governs both living and nonliving matter.

    We can now see how life simply results from electrically interacting atoms. DNA, and all of its chemistry, operates through the electrical interactions among atoms and molecules. The DNA molecule formed because it is a naturally stable configuration of electrically interacting atoms. In the same way that two protons join to form a nucleus of a helium atom because their combination forms a stable arrangement of interacting particles. Similarly, water molecules occur because they are a stable arrangement of atoms. If two atoms cannot be joined then they will not; if they can join then they will. DNA molecules formed because they too are a naturally stable configuration of electrically interacting atoms.

    DNA naturally formed in the past and developed though time and the generations of its self-duplication process. It naturally divides, reproduces, directs chemical reactions, and changes through successive generations. Whenever this combination of atoms occurs, this is what they are going to do. The changes that make DNA–and its resulting individual–better matched to its environment of climate, predators and food result in increased chances of that individual, being around long enough to reproduce itself.

    All life on earth is composed of the same basic twenty amino acids, five nucleotides, two sugars, glycerol, choline, and palmitic acid. These build 120 other amino acids, thirty-six sugars and nucleotides, numerous fatty acids, proteins, RNA, and DNA. RNA stores the genetic information and initiates actions. RNA may have been an initial life form that evolved into more efficient DNA (information) plus proteins (actions).

    The same chemical reactions that occur inside life-forms also occur in laboratory dishes. A "living" blob takes in one chemical and obtains energy from it by dividing it into simpler chemicals which it uses for other things and then expels. These sorts of machines have been made in the laboratory. For example, surround chemicals A and B with a membrane of chemical C. A certain chemical D will pass through the membrane. Once inside, chemical D releases energy as it is broken into chemicals E and F. These last two chemicals might either be used internally in additional reactions, or flow out of the membrane. Notice also that there is nothing special about any one of the atoms within our bodies; in fact, they are constantly being replaced with others. Individual atoms are typically replaced every eighteen months.


Science, living matter, and religion


We can now summarize the steps that lead to life: the Big Bang was soon followed by protons, neutrons, and electrons that formed into hydrogen and helium atoms, some of which then coalesced into stars. Stellar fusion and supernova explosions create the heavier elements, including those now found within your own body. Chemistry occurs through the electrical interactions of atoms. Carbon atoms are able to combine into long chains and rings containing hundreds of atoms. Biology is largely the chemistry of carbon. Two joined molecule-strings of carbon and other atoms resulted in a self-duplicating, self-growing, and self-directing molecule. This is life.

    Life is a collection of molecules. It is what naturally results when hydrogen, carbon, oxygen, and various other atoms are allowed simply to mix for a while. Stable combinations of carbon atoms occur, and through time, collections of such combinations grow in size. Self-directing, self-building, and self-operating molecules (life) soon occur.

    Through a few billion years of collisions, combinations, and alterations, the earth's molecular life forms grew in length at a rate of about one atom per year. When life grew to contain one billion atoms, it had become large enough to see without having to use a microscope. As mentioned above, the Earth formed about 4.5 billion years ago. It is likely that self-duplicating molecule-machines developed on the earth in the first few tens-of-millions of years. Four billion years ago, our ancestors existed as these little molecule machines; this means that today's amoebae are our cousins. Life on earth remained microscopic for almost four billion years–eight-ninths of its history–before the first multicellular life-forms developed. Plants, fish, insects, reptiles, birds, mammals, primates, and humans have rapidly appeared during the last 750 million years–the most-recent, one-ninth of its history.

    A self-duplicating and self-operating collection of molecules will grow in number if it functions ably within its surrounding environment of climate, predators, and food. Any change that makes a certain molecule-machine better matched to its environment will naturally result in further generations and an increased number of that type of molecule-machine. If a change makes the molecule-machine work less-well then there will be decreasing numbers–or even an extinction–of that type of molecule-machine. Each change will be followed by additional changes. Evolution is the buildup of changes that began with the first self-duplicating molecules.

    We can now see what is meant when it is said that humans are an example of a complicated end-product that occurs by combining a very large number of simple, natural phenomena–mostly involving electrical interactions among atoms. It is sometimes said (by physicists) that biology and chemistry are additional aspects of physics because chemicals, plants, and animals are just systems of electrically interacting atoms. Remember that Schroedinger's equation (see Chapter 2) is the version of Newton's law that describes the motions and energies of interacting atomic-sized objects and that Maxwell's equations describe the electrical force in all systems. The combined Maxwell-Schroedinger equation (or atomic-electrical equation) describes the electrical interactions among the atoms of both living and nonliving matter–with no distinction. No additional law is needed to describe the atomic interactions within living matter. Life consists of the chemistry of these self-duplicating, self-directing, and self-growing, electrically interacting molecule-machines. The fundamental functioning of these molecule-machines is completely determined by the known law of physics describing the electrical interactions of atoms. Life occurs naturally: it is part of nature.

    This atomic-electrical equation makes it easy to determine the force between two charged particles and allows us to understand how molecules form. Nevertheless, it doesn't give an easy way to predict ahead of time which geometrical shapes or combinations of charged particles will form a stable molecule having a stable shape. We have to resort to a lengthy, trial-and-error search for stable configurations. Molecules naturally form when their geometrical size and shape consists of a stable combination of electrically charged atoms: since they can form, they do–in fact, they must. There is just one law of physics that describes the electrical forces within every existing material structure but we have no easy way to predict what sorts of organizations of matter will occur or can be built with these known forces. This is true of every physical force behind every level of organization of matter, from elementary particles and nuclei, which form through the strong force, to the electrical force that builds atoms, molecules, 20-atom carbon rings, 400-atom proteins, billion-atom DNA molecules, tissues, organs, individuals, and societies. Neither does the atomic-electrical equation easily describe or predict the overall, large-scale properties of a group of billions of atoms. That is, we don't describe a tissue by applying Newton's Laws (written as a Maxwell-Schroedinger equation) to the electrical interactions between each pair of its atoms; instead, large-scale rules are found to describe more-easily the entire structure and its overall properties.

    The value of the statement that the atoms of biology operate through the physics of electrical interactions is that no new or additional laws are needed to explain the fundamental, atomic basis of biological phenomena. The electrical interaction between the atoms of a liver is not different than the electrical interaction between the atoms of a rock or transistor. Living matter does not follow different physical laws than does nonliving matter.

    The Schroedinger equation describes the time-evolution of any arrangement of interacting atoms and molecules. This equation is usually solved with the aid of a computer, except that today's computers have the capacity for only the simplest problems. There is a lot of chemistry that cannot yet be approached this way. The last fifty years of improvements in computer technology have allowed the number of modeled, interacting particles to increase from ten to just 100,000. I imagine that after another fifty or one-hundred years, computers will have the capacity to solve Schroedinger's equation for DNA molecules, and a while later, for single-celled life-forms. Within a century or two, high school students will run computer programs that model–at the atomic level–all the chemical and physical processes occurring within a person. This will verify our complete understanding of biological molecule-machines.

    Both living and nonliving matter are part of nature. Nature consists of nonliving molecules and it also consists of self-directing, self-growing, and self-reproducing–that is, living–structures built from billions of molecules. Molecules form as groups of atoms because they can. Life occurs because it can–because it too is a part of nature. The laws of nature result in life. It makes natural sense that whatever can produce further generations, does produce future generations. Some Christian, Muslim, and Jewish scientists feel that this allows them more-fully to appreciate God's creation.

    All of today's major religions emphasize the same ideals of ethics and morals. In addition, the half of us humans who are followers of Judaism, Christianity, and Islam believe that there is a supreme being. We have just seen that life is a natural process. Does this mean that God does not exist? Actually, it doesn't say anything about God. You might say that God created life by creating the natural laws of the universe, or maybe, that God is the natural law of the universe. She knew that the universe would occur, chemicals would form, and a little while later, you would form. This is consistent with the recent Vatican statement that evolution does occur but God is the creator. Scientists are not out to prove or disprove the existence of the Supreme Being, they simply want to know how the universe operates. Some scientists explain that their goal is "not just to believe in God but to know the mind of God." Many of those of us humans who live in the Eastern half of the world have never taken the idea of a Supreme Being and so have trouble understanding the cause of the tension that can exist between science and some religions. The scientist, the Western theologian, and the Eastern theologian all have the same goal: to understand the universe and to live a moral life–and they are each equally ethical persons.

    Science and religion rarely discuss the same topic. Scientific topics–the details of nature–and Bible topics–how to behave in life's situations–do not often overlap. Scientific knowledge rarely describes potential behaviors in particular social situations and the Bible does not contain a detailed description of the fields of science and technology. For example, it does not contain a blueprint for a medical x-ray machine. When our theologians analyze the occasional descriptions of natural phenomena given in our sacred texts, they might see that these descriptions are consistent with the facts of nature that have recently been measured to be true. Three thousand years ago, the sacred Hebrew texts explained human interactions in terms that the followers could understand at the time. I am sure it contains information that agrees with today's understanding of the natural world. For example, the Bible says "God created man in his likeness." Some say this refers to a moral likeness. I don't know what this means exactly. Maybe it's referring to the fact that we are made of electrically interacting atoms just like Him. Is God made of atoms? Did God create the natural rules that govern atoms and so cannot be made of atoms? Such questions require the expertise of theologians.

    Science, and its large number of measured facts, increases the awe and respect we have for nature and the beauty we see in nature. As we look more closely, we begin to see the intricate workings that go on in nature. We also see how nature consists of a few simple rules, and how these simple rules result in an incredibly complex and interrelated world. This increases our amazement of nature. For those of us in the world who believe in a Supreme Creator, science actually increases our appreciation of the Creator's natural rules and of the resulting world.


Evolution


We all know that plant and animal types vary with climate. As one travels from warm to cold latitudes or elevations, changes in tree type are seen. For example, while traveling from Florida to Canada one finds a change in tree type from palm trees to pine trees and then to maple trees, and there is a change in animal type from alligator to moose to polar bear. It naturally occurs that through time, the range of each type of plant and animal moves northward and southward with each glacial advance and retreat.

    It occurs that there is a range in each characteristic of the individuals of each species of plant or animal. For example, we all know that there are ranges in the size, speed, agility, eyesight, hearing, and heights of humans, and there are also ranges in the ability of individuals to digest certain foods or to handle cold or hot weather. We all know someone who says that carrots or cold weather do not agree with them. There are variations in characteristics from one individual to another. A range in the characteristics of the individuals of a species occurs because of the underlying range in the genetic makeup, or DNA, of those individuals.

    Whenever there is a change in the environment then there is also a change in the characteristics best matching the requirements of the environment. The average characteristics of the individuals of a species change in time as the environment changes in time. For example, as described above, the Earth's continents slowly move about the planet, resulting in changes in climate on each of those continents. In turn, changing climate results in changes in plant and animal types. In an example important in our own past, we’ll see below that a developing geologic rift resulted in a drying East African climate and subsequent changes in food sources for our ancestral primate species, which in turn became changed.

    Variations in the individuals of a species occur and are tested for usefulness by the environment of climate, predators, and prey. The environment does not produce these changes, it only tests the usefulness of the existing variations in the characteristics of the individuals of the species. The useful traits continue to get passed on to future generations simply because future generations are then able to occur. The individuals that are better-matched to the environment will likely produce more offspring than do the less-well equipped individuals, and this results in a shift in the average characteristics of that species. After several such adjustments, the species will have changed significantly: it will have evolved. As mentioned above, some changes–that is, evolution–in plants and animals occur because of changes in the environment–which consists of climate, predators, and food–while other changes occur because of chemical errors that sometimes happen when a DNA molecule is duplicating itself or when DNA is damaged by external radiation

    This has resulted in Darwin's principle of evolution: if the traits of an individual make it better matched to its changing environment of climate, predators, and food, it is then more likely to live long enough to have its own children. In turn, these traits will be passed on to the resulting future generations simply because future generations will occur. In the extreme case of a particularly bad trait, which results in a quick death, there will be no children: this trait disappears. The environment naturally selects those individuals possessing the traits best matching the environment. Visit http://pages.britishlibrary.net/charles.darwin3/darwin_bio.htm for a biography of Darwin and to view an on-line copy of his original publication.

    Darwin's principle is about 150 years old. Already by 150 years ago, the evolution of species was evident to us even though we had made but a tiny fraction of the observations and measurements that make up today's biological knowledge. Biologists have recorded millions of such changes and use the word "evolution" because a sequence of changes has been observed to have already occurred. The principle of evolution explains those millions of observations.

    Whenever you hear the word "evolution" you should think of "changes in the most-appropriate traits due to changes in the environment of climate, predators, and food." Evolution is about becoming better matched to the environment and is not about becoming more complicated, improved, or stronger; such things may or may not occur. Notice also that emotional and behavioral traits are also subject to evolution because the traits of the entire individual must be appropriate to the individual's environment. We’ll see more about this later.

    Today we understand more completely how DNA and its genetic information produce each of our traits. In fact, scientists have found that the answer to every biological question is given in terms of DNA and how well its resulting individual is matched to its environment of climate, predators, and food. Each time a change in a species is observed, biologists look for the reason that that change made the individuals of the species better matched to their surrounding environment. During an experiment involving a species having a life span of just a few days, as does the fruit fly for example, biologists will observe many successive generations in a short time and see rapid changes occur in that species.

    Evolution is the answer to every question in biology; it has answered millions of questions. Millions of times per day, biologists are using evolution to explain an aspect of life. This means that about a million times per day, the idea of evolution is successfully explaining specific aspects of life. This makes evolution a successful theory. Any alternative explanation must also explain each of these millions of measured facts concerning life.

    A change in the environment can present new opportunities for some species. Whenever new opportunities begin to emerge, nature–that is, the environment–will test the variations in the traits of the existing individuals. A portion of the existing species will be genetically equipped to take advantage of those new opportunities. Since each species has its own food sources, competitors, variations among individuals, and chemical errors, what is an opportunity to one species will not be an opportunity to all species. These other species may remain unchanged. When a specific example of how one animal changed to take advantage of new opportunity is given, it doesn't mean that every type of animal would also change in that same way. If that occurred then all animals would soon become identical–and extinct. It is always the case that just a portion of species change when an opportunity emerges. This is how tree-dwelling prosimians developed clasping hands while tree-dwelling squirrels did not.


The sequence of life forms that have evolved on the Earth


We want to know what were the stepping stones that turned our biological ancestors into us. We also want to know in what ways we are similar to other animals and in what ways we are different from them. Examining the evolutionary relationships and the similarities and differences between ourselves and other species helps us develop a more accurate notion of what it is to be human. To this aim, we next have a brief look at the sequence of plant and animal types that have occurred on the Earth along with the sequence of changes that produced those animal types. We’ll see that the largest changes involved the development of new organ systems, one by one, over the course of a few hundred million years. Today, we have sensory, digestive, skeletal, circulatory, and nervous systems along with a means of temperature control. Except for some ability to react to the surroundings, the most-primitive life forms have none of these. A new category of animal occurred as each of these systems first developed. The time-order of appearance of the major categories of the Earth's plants and animals has been determined from measurements of the age of fossils and of their excavated surroundings. The time of occurrence of each of these events were determined using radioactive dating (described above), relative dating (see http://pubs.usgs.gov/gip/geotime/fossils.html), or by various other means (see www.geo.arizona.edu/palynology/geos462/11datingmeth.html.) Scientists categorize fossils into groups of animals having similar structure. The similarities and the differences provide clues for deeper understanding–for example, of which species are adaptions of which others.

    Through the last 750 million years, millions of species have come and gone. A typical species exists for a few million years before either disappearing or evolving into another. Some species exist for a much shorter time span while others last longer. Some ancient species still exist today but the vast majority have had a temporary existence. For each species existing today, one hundred have come and gone in the past.

    Paleontologists have found millions of fossilized animal remains. As they first started finding fossils a couple hundred years ago, scientists constantly found new fossil species that had never before been seen. Eventually, new excavations resulted only in additional copies of already-known fossil species. As they stopped encountering previously-unknown fossil species, they knew that they were beginning to have a fairly complete picture of the past. In the last few centuries, thousands of biologists have spent their entire lifetimes studying millions of living and fossilized plant and animal species. The University of California Berkeley website has a video at www.ucmp.berkeley.edu/education/explorations/tours/fossil/9to12/intro.html which explains that one becomes a fossil by waiting a long time.

    Scientists determine the time at which each fossil species appears and then later disappears. This reveals the time-sequence of changes in plant and animal species. Each fossil skeleton is like a snapshot of the development of an animal species: a series of snapshots forms a movie. The observed time-sequence of small changes that have occurred for each species shows they are evolving through time. As described above, changes in species occur through genetic mutations or in response to changes in predators, food, or climate.

    A single fossilized tooth can tell a scientists much about an animal. For example, animals that eat meat have sharp tearing teeth while those that eat plants have flat grinding teeth. These distinctions also help us know the type of food eaten by each of our ancestral primate species. If a single tooth is handed to certain scientists, they will be able to identify the species of its owner because the size, shape, material, mounting, type, and number of teeth are unique for each species. 

    The relationships between species are evident in many ways. For example, the embryos of various vertebrates show many similarities. (For a morphing video of a growing mouse embryo, visit http://embryo.soad.umich.edu/animal/animalSamples/mouseMorph.mov. The PBS website has movie clips at www.pbs.org/wgbh/nova/odyssey/clips showing the development of an embryo from each of several species, including humans. Visit www.indiana.edu/~anat550/embryo_main for animations of developing embryos, including the emergence of a human face.) The embryo of an animal often contains reminders of its earlier forms: human embryos temporarily have tails, while other terrestrial, vertebrate embryos temporarily have gills. The skeletons of all vertebrate animals–including fish, amphibians, reptiles, and mammals–share much in common, consisting of backbone, ribs, limbs, neck, and head. Their overall similarity suggests that they are closely related. At a finer scale, the bones of all mammals share much in common. For example, nearly every mammal, from mouse to giraffe, has seven vertebrae in its neck–despite the range in size of the mammal.

    The common ancestry of diverse animals is made evident by specific aspects of their DNA. Scientists have found that the gene causing the development of a specific body part–for example, an eye–is identical throughout a large range of animals. If the eye-creating gene is removed from the DNA of a fly larva then that fly develops no eyes as it grows into an adult. If the eye-producing gene of a fly is removed and then replaced with that of a mouse, the fly will again grow to have eyes. It will have the normal, compound eyes of a fly and not the eye of a mouse because other genes direct the building of the components of the eye. This shows that flies and mice–insects and mammals–share a common, eye-bearing ancestor.

    Animal brains share features due to their common ancestry. Our human brain consists of three sections. One section is the oldest mating-and-aggression part and is found in every reptile species and in every species that is a descendant of the reptiles. The second brain section is the early mammalian part that produces our emotions and is common to all mammals. The third section in the human brain is used for our thinking processes.

    As stated above, it took about four billion years for the earth's microscopic life to develop into the earliest forms that had become large enough to be seen with the unaided eye and to become organized into cells. All of the Earth's life forms are the descendants of its earliest molecule-machines. Scientists have found examples of life that occurred three billion years ago. These Eobacterium were 0.0002 inches in length (five micrometers) and contained a double-layered cell wall similar to that of modern bacteria. Bacteria are the Earth's most primitive, larger-than-molecular form of life. The earliest types do not contain a distinct nucleus housing their DNA.

    Sexual reproduction is also very old, beginning about two billion years ago. This mixing of genes from two individuals provides for increased variation in the traits of offspring. This increased variation means that a wider range of traits is already in place so that the species will more-likely be able to continue even when there is a sudden change in the environment. 

    Single-celled bacteria are the Earth’s most primitive life form. They obtain energy for life by taking in particular chemicals and releasing others. Some types of bacteria live at temperatures of 100, some at zero, and others at -100 degrees centigrade (corresponding to 200, 30, and -200 degrees Fahrenheit; Fahrenheit was a scientist who studied heat). Some types require air and some do not. For example, the E. Coli that live in our stomachs and help dissolve food into its constituent chemicals do not require air to live. There are types of bacteria that live in either acid or salt solutions. Every life form on the Earth requires liquid water–neither frozen water nor steam is usable–and chemical or solar energy. (We saw above that life mostly consists of the molecules carbon, oxygen, nitrogen, and hydrogen.)

    Life forms employ three strategies in obtaining energy. Plants convert sunlight directly into chemical energy while animals either eat (ingest) plants directly or eat those other animals who eat plants. Fungi instead selectively absorb chemicals directly through their surface as they breakdown dead organic material. Examples of fungi include molds, single-celled yeast, and mushrooms. Yellow algae are single-celled plants while an amoeba is a single-celled animal. Lichens are a symbiotic combination of a fungus and a photosynthetic algae and are often seen as the coatings on rocks.

    About 10% of all sunlight falling on the Earth is utilized by plants, about 10% of the chemical energy stored in plants is later utilized by the animals who eat those plants, and 10% of that energy is utilized by carnivores who eat the plant-eaters. As my friend Zen points out, sunlight powers the plants; in turn, plants power the animals that eat them–and the animals that eat the animals that eat the plants, too. In this way, sunlight powers all life on Earth. This process has daily and seasonal cycles, as seen in the NASA video clip at http://svs.gsfc.nasa.gov/search/Keywords/Pulsing.html.

    During the photosynthetic process, chlorophyl molecules within plants absorb sunlight. (Through the season, plants appear more green and then less green as the number of manufactured chlorophyl molecules increase and then decrease.) The absorbed sunlight interacts with water and carbon-dioxide, which was previously absorbed from the atmosphere, to form sugar (glucose) and oxygen, which is released into the atmosphere. Sugar or glucose stores the absorbed solar energy for later use. The DNA of a bacterium has the information needed to convert glucose into each type of organic molecule that the little creature requires in life. (Some creatures manufacture their own amino acids, carbohydrates, and lipids while others must instead selectively absorb them through their surface.) Sugar or glucose is a mixture of equal numbers of carbon atoms and water molecules. A string of sugar molecules form polysaccharides, such as starch, which is found in potatoes and corn and such, and cellulose, which forms tree trunks, plant stems, and leaves and such. By the way, photosynthesizers don’t have to move to collect food because it rains down on them as sunshine, but plant eaters do have to move.

    When animals eat food, it is broken down (digested) into chemicals such as glucose and stored within each cell. We humans produce an enzyme that breaks the animal starch glycogen (a component of muscle) into individual glucose molecules but we can not break plant starch into individual glucose molecules. That’s why we eat animals but do not eat leaves, grass, or tree trunks. Animals needs energy to keep warm and to move; we use one hundred calories per mile (1.6 km) walked. Animals inhale oxygen and transport it to each cell where it is combined with stored glucose obtained from the previously eaten and digested food. This combination releases energy in the form of ATP molecules while also producing carbon-dioxide, which is then exhaled. The more energy we need, the more rapidly we breathe and exhale. The glucose and oxygen are combined in mitochondria, which are a special-purpose organelle within each of our cells. (About one billion years ago, cells developed various, special purpose sections, which are called organelles, and a nucleus that contains their chromosomes. For illustrations of cells and cell parts see http://ghr.nlm.nih.gov/info=Illus.) The doubly ionized oxygen atoms that result from the respiration process sometimes manage to get into the cell nucleus and damage DNA, but the damage is often found and removed in the bump-detection process described above.

    A cell absorbs and flushes chemicals through its surface. The entire volume of a cell must be kept in close contact with its surface in order for chemical reactions to occur throughout the cell. As the size of cells increase, their volume grows much more quickly than does its surface area. The size of a cell must remain microscopically small because its chemistry is limited by its surface area. My friend Zen explains that the only way for life forms to be larger than microscopic in size is for it to become multicellular. Sponges are a collection of individual cells, each of which could exist on its own. Seaweed and kelp–which are green, red, and brown algae–are examples of primitive multi-cellular life, as are moss and liverwort plants.

    An early, multicellular plant consisted of an aboveground short vertical stem for photosynthesis, and a belowground portion, one foot (30 cm) or so in length, that obtained nutrients and water from the soil. The stems had short horizontal branches and some woody tissue. Plants developed a vascular system to carry nutrients between these two portions. Later, seedless plants with leaves developed–the spore-bearing ferns, for example–and were followed by plants with needle-like leaves, seeds, and pollen–for example, the conifers such as pine, spruce, and redwood. At first, seeds were uncovered but later they became enveloped in a fruity material. This attracts animals who carry the fruit away, inadvertently helping the plant to disperse to other areas.

    Flowers are a modified leaf. There were no flowers until just twenty-five million years ago. This means that there were no flowers or grasses during the time of the dinosaurs, and their absence would have made the landscape seem unfamiliar to us. Grass evolved from flowering plants. In turn, this led to the development of grazing animals. It is surprising that grasses and flowering plants, and the interaction between insects and flowering plants, are relatively new. Before there were grasses there were no grass-eating animals. Every change is quickly followed by additional changes.

    Metazoans are multicellular animals that first occurred some 700 million years ago. They have a variety of cells serving a variety of functions, have tissues and organs, and are soft-bodied animals such as anemones and jellyfish. Their fossil remains have been found in many regions of the Earth. A collection of very early and especially strange creatures were found in the geological deposits of the Burgess Shale. To view animations of these creatures, visit either http://www.gpc.edu/~pgore/geology/geo102/burgess/burgess.htm or the website http://homepage1.nifty.com/burgess/aa.html. For a video with an accompanying musical score, visit the website http://rand.info/rands/text/notes/burgess_shalen.html.

    Zen Buraceski explains how a sequence of changes in body shape changes jellyfish into winged insects. DNA controls the size of animals simply by controlling how long they grow, chemically signaling when it is time to stop. DNA controls the shape and symmetry of every plant and animal species, including jellyfish. Visit www.arkive.org/species/ARK/invertebrates_marine/Aurelia_aurita/Aurelia_aurita_00.html to see a video clip of jellyfish or www.photolib.noaa.gov/reef/reef2547.htm for a jellyfish photo. With a small change in DNA, round jellyfish bodies become rectangular flatworm bodies. (Visit www.photolib.noaa.gov/reef/reef0198.htm for a photo of a flatworm.) The body of a roundworm results when the body of a flatworm is rolled up, as seen at www.arkive.org/species/invertebrates_terrestrial_and_freshwater/Lumbricus_terrestris/ARK007780.html. Mollusks develop if instead a shell is secreted from the body. A video clip of a giant clam can be seen at www.arkive.org/species/GES/invertebrates_marine/Tridacna_gigas/Tridacna_gigas_00.html. Segmented insect bodies develop by adding legs to segmented roundworms. (To listen to various insect sounds, visit http://cmave.usda.ufl.edu/~rmankin/soundlibrary.html.) If a protrusion emerges from one of those segments (www.arkive.org/species/ARK/invertebrates_terrestrial_and_freshwater/Calopteryx_splendens/ARK018717.html) then a winged insect results. Still another type of animal (fish) develops from a roundworm by adding first gills and later a mouth and fins.

    You might like to explore the tree of life further at http://tolweb.org. You might also search PBS videos at www.pbs.org/wnet/nature/database.html and www.pbs.org/wgbh/nova for one-minute clips of various animals and their behaviors. Movies of various microscopic creatures, from amoebas to worms, can be seen at http://micro.magnet.fsu.edu/optics/olympusmicd/galleries/moviegallery/pondscum.html. The NOAA website has photos of various plants and animals at www.photolib.noaa.gov/reef/index.html.

    Scientists see that as animal forms have evolved in time, a series of particularly successful types emerged because they had each developed an additional organ system. By adding additional systems, one-by-one, onto those already existing, the resulting sequence of animal types form the stepping stones from bacteria to today’s species. One after another, the sensory, digestive, circulatory, neural, and skeletal systems were accumulated. Another important development was the improved means of temperature control, which is one of the distinguishing features of mammals and birds. In the next few paragraphs we'll see that shellfish are the earliest animals to have digestive and circulatory systems and increased senses, that nerves and senses are yet more developed in insects and spiders, and that the back-boned animals (vertebrates) developed a central nervous system. Millions of species have come and gone during this time because of the ever changing environment of climate, predators, and food.

    The first invertebrate shellfish appeared about 700 million years ago. These soft-bodied animals secrete a shell that supports and protects them. They have digestive and circulatory systems and a nervous system that reacts to sensations. These mollusks include oysters, clams, mussels, snails, and squid. Today, there are 110,000 species of mollusks. There are only half as many vertebrate species.

    Highly specialized nerve and sensory systems first appear in the arthropoda animals. These represent about 80% of today's animal species and include insects (which have six legs and include beetles, ants, and butterflies), spiders (which have eight legs), centipedes, crabs, shrimp, and lobsters. These animals have either single-lens eyes, compound eyes, or none. You have eyes because you are their descendant (the eye-producing gene of flies and mice–insect and mammal–was mentioned above ). Numerous arthropoda species came on the scene between 600 and 225 million years ago, including the previously-common trilobites. You'll see many trilobite fossils when visiting museums or the website www.biol.wwu.edu/trent/alles/Trilobites.pdf.

    An early form of backboned vertebrates had a hollow, central nervous system, gill slits, tail, and a circulatory system with a pumping heart; this is the reason you have a backbone and a heart. It is a descendant of filter-feeding worms that had slits to allow food-laden water to enter and exit. This led to fish and then to all the vertebrates that live in the water and on the land. The gill slits were mainly for filter-feeding but also helped obtain oxygen. (Older life-forms, such as diatoms, obtain oxygen directly through their outer surface.) Its food is trapped in mucous and then moved into its gut for digestion. These animals were typically 10 inches (25 cm) in length and were much larger than the average invertebrate.

    The fish first appear about 500 million years ago. The earliest fish have a rudimentary brain formed from a clump of nerves–this is the reason you have a brain–and they had gills for filter-feeding. Initially, fish had no jaw but soon, some of its gills developed into a jaw. For a video clip of jawless fish, visit www.arkive.org/species/ARK/fish/Lampetra_fluviatilis/Lampetra_fluviatilis_07.html. Still later, one gill arch-support became the ear bones that enable us to hear and yet another support enabled a movable tongue. You might notice that a shark's (for a live webcam, see http://waquarium.otted.hawaii.edu/coralcam/index.html) mouth is still underneath its body and has the V-shape of a gill. (Nature has found frequently that it is much easier for an existing structure to become adapted for a new purpose than for an entirely new structure to develop from nothing.) An illustration showing a jawless fish and the bones which would become a jaw can be seen at www.museum.vic.gov.au/dinosaurs/image_html/mn001429.html. The bone-supported jaw allows for biting and grasping and provides the ability to eat larger things. Jawed fish were able to out-compete jawless fish, and thousands of species soon developed. Fins and scales were next to develop.

    In the last 500 million years many variations in fish have developed. Some fish developed organs that produce venom while others produce light or electricity. Flying fish can glide through the air for short distances above the water. The walking catfish of Florida move short distances on land. Another fish encases itself in a cocoon and then buries itself to survive for months beneath the dried up remains of a pond while waiting for rain to refill the pond.

    The Choanichthyes were the first animals to emerge from the water and move onto the land. For an image of an Ichthyostega, see http://www-biol.paisley.ac.uk/courses/Tatner/biomedia/pictures/ichth63.htm. See also, http://tolweb.org/tree?group=Ichthyostega&contgroup=Terrstrial_vertbrates. They likely developed fingers before leaving the water, see www.pbs.org/wgbh/evolution/library/03/4/l_034_03.html . It may be that initially they were leaving the water to avoid predators or to move between receding puddles. Fins began to be used as legs. The osteolepis had four fins that became the four limbs of its land-based descendants. (Imagine what humans would be like if we had inherited six limbs instead of four. For example, we might be able to drive a car, talk on the phone, and change a baby's diaper all at the same time). There is a continuity in the skull bones of fish and amphibians. In the roof of their mouth, the Choanichthyes fish had a pair of openings connected to external nostrils. Both the Choanichthyes fish and lungfish, who have both gills and rudimentary lungs, were more common in the past than today. That rudimentary lung has become the swim bladder of the modern fish and is used for hydrostatic balance.

    A number of changes occur as animals adapt from life in the water to life on the land because the two environments are very different. For example, an animal's body can dry up when it is no longer surrounded by water. Also, since the buoyancy of the water is no longer supporting the animal's weight, more supporting bones are needed, and an increased metabolism will be needed to provide the increased energy requirement that this entails. As a plant-eating animal migrates from water onto land it will find that its usual food is very different, and this will require changes in its digestive system. There is a much wider range between nighttime and daytime temperatures on land than there is under the water. The change in environment required many changes in the body, including the enlargement of lungs and the replacement of gills. Nasal passages became enlarged for better breathing and a better heart, having three chambers, emerged for increased circulation. (To view a movie of a beating heart, visit http://sln.fi.edu/biosci2/monitor/video/echo.mov.) Eyes were no longer immersed in water so they developed eyelids, glands, and lubrication ducts, all of which keep eyes free of foreign objects and protect them from the glare of the sun. There was pectoral and pelvic strengthening to support the increased body weight and a strengthened attachment of the internal bones that support limbs. A neck developed to allow the independent movement of the skull. The spinal column became sturdy but flexible. Old gills became efficient vibration detectors (ears). Scales disappear except along the underside that scraped the ground. The number of skull bones decreased from 140 to just 27.

    These changes required about fifteen million years to occur and resulted in amphibians, such as toads, frogs, and salamanders. Soon, some land-based reptiles moved back into the sea, looking much like the later mammals who moved back into the sea to develop into whales and dolphins and such. Amphibians lay fish-style eggs in water and their young begin life with gills. We all know, for example, that tadpoles hatch from eggs and become frogs.

    Reptiles developed from amphibians. While amphibians lay soft eggs in water, reptiles lay hard-shelled eggs on land. The egg of a reptile contains its own "pond." The egg contains food for the growing creature, and its soft shell allows air to flow in and carbon dioxide to flow out. The dinosaurs were reptiles, as are today's snakes and lizards. (For some animations, visit www.amnh.org/exhibitions/dinosaurs/theropod/walk.php, www.nmnh.si.edu/paleo/dino/trinew.htm and www.amnh.org/exhibitions/dinosaurs/sauropod/apatosaurus.php. For information about creating animations, see www.amnh.org/exhibitions/dinosaurs/sauropod/morphing.php.) A reptile's legs are on the side of their body so that they walk by twisting left and right, swinging their legs outwards like oars. In contrast, the legs of a mammal are underneath their bodies, allowing for better support and movement. Both birds and mammals are descendants of the reptiles. There were lizard-hipped and also bird-hipped dinosaurs. There are known examples of mammal-like reptiles that led to mammals. Mammals are a direct descendant of reptiles. In other words, one can say that reptiles are the link between amphibians and mammals.

    A little while after the dinosaurs became extinct, mammals increased in abundance by out-competing the remaining reptiles. They did this by acquiring an improved nervous system and increased speed and agility. The first mammals ate insects, as do today's shrew and mole. We humans are still able to digest insects, though many cultures prefer not to. Except for birds and insects, the animals that we most often see every day are mammals. Every four-legged, furry animal is a mammal, as are humans.

    Mammals differ from reptiles in a number of important ways. Mammals have hair and sweat glands for body-temperature control, and a larger portion of their body weight is due to their brains. Instead of laying eggs, mammals internally incubate their young and then give birth to live young. Mammals have mammary glands for feeding their young, and, most importantly, they have a parenting reproductive strategy in which they take more personal care of their young than do egg-laying reptiles. This strategy is in contrast to most non-mammals who are not parents in that adults typically leave behind a batch of thousands of eggs to tend for themselves. The adult never knows its offspring, and just a small portion of those thousands of abandoned offspring survive to become adults themselves. Since this attention makes their young more likely to live beyond childhood, mammalian liters contain fewer individuals than do those of non-parenting species. The lack of parenthood among other animals will also mean they have a lack of parenthood instincts; they worry only about their own lives.

    Mammals have a child rearing strategy in which they protect, teach, and rear their offspring through infancy until they in turn become old enough to have their own children. We have seen that natural selection means that those individuals whose traits are better matched to their environment of climate, predators, and food will be more likely to live long enough to have offspring. Franz Dewaal points out that for mammals, the most-genetically fit individuals are those who are matched to their environment and successfully rear their children to the point that they in turn are prepared to raise their own children. Mammalian parenthood is a large part of the human animal. We will discuss this many times in the coming chapters.

    Mammals are also much better at communicating than are reptiles. They make it obvious that they are friendly, are going to attack, or that they are happy, sad, or angry. I can understand the face and posture of other mammals–for example, those of a growling dog–but I communicate little with insects or reptiles. Some exceptions include understanding the threat of a scorpion's tail or of a rattlesnake's noise and strike posture. I know when to run from the tiny growling dog but I can't seem to communicate at all with my friend's pet iguana.

    Scientists have cataloged 4,000 species of mammals, 9,000 bird species, and about one million insect species. All together, more than 1.5 million animal species have been studied, but this is only a fraction of the existing species. The total number of animal species is estimated to be anywhere between two and ten times the number already studied. (By the way, the total mass of all the Earth’s plants far exceeds the total mass of animals.) And for each species existing today, it is estimated that one hundred have come and gone in the past. A species typically exists for a few million years before becoming extinct but some last one hundred times that long. If you line up a series of two hundred species’ lifetimes, each lasting about three million years, then the series will extend through 600 million years, which is about the amount of time that has elapsed since multicellular life developed. Hence, very roughly speaking, we can say that a sequence of just a couple hundred species-sized modifications can change bacteria into humans. We also see that humans are not too different internally from mice and other mammals. In the next three chapters, we’ll see that we humans are also behaviorally similar to the other mammals–especially to the other primates.


 Summary


In summary, life occurs naturally as collections of electrically bound atoms become self-duplicating, self-growing, and self-operating. It took about four billion years for the Earth's microscopic life forms to grow to visible size. The sequence of stepping-stone animal forms that have developed in the last 750 million years includes non-boned invertebrates with eyes and a sense of touch, fish with bony skeletons and hearts and brains, amphibians that left the oceans for the land, reptiles that lay hard-shelled eggs, and parenting mammals. Mammalian parenthood is a large part of the human animal. We humans share organ systems, skeletal structures, and senses with other animal species. We see that we share common ancestors with every other species–from amoebas to whales. Visit www.pbs.org/wgbh/evolution/about/overview.html to view a video clip of Jane Goodall explaining our evolutionary relationship with the other animals of the Earth. This is part of the eight-hour PBS documentary Evolution.

    Animals also have similar emotions. In the coming chapters, we will see that our most ancient behaviors are hormonally induced, just as they are for other animals. For example, a drop of adrenaline helps us to flee and to ignore pain. We contentedly chew cherries. Our taste-buds produce a pleasant feeling when eating useful foods. We also have pleasant feelings while performing useful actions ("useful" actions are those that make it more likely that we will live long enough to have children). Does a cat experience a pleasant feeling while it is cleaning its fur? Will a bee experience a pleasant and contented feeling while it is walking on flowers? (It walks on flowers to gather pollen, which it uses to make honey. Its taste buds are located on its feet). How can we measure answers to questions such as these?

    Again, the PBS televison series Race, see www.pbs.org/wnet/dna/episode3, discusses genes and race: a person's appearance–ear shape, hair color, height potential, skin color, nose size, and eye shape and such–is determined by perhaps one part in one-thousand of his or her genetic makeup. Where we instinctually place much weight on the outer appearance of an individual, we are analyzing but a small fraction of that individual's genetic makeup. The vast majority of our genes produce our bodies with cells, arms, legs, eyes, hearts, and livers and the other organs. This means that two human individuals are 99.9% genetically identical. Two unrelated individuals differ by only about 30 out of 30,000 genes, which is a difference of 0.1%. This is true whether or not those two individuals are of the same race, come from the same hometown, or come from opposite sides of the Earth. We now know how thoroughly we share the genes that make us human. Two siblings differ by half of that 0.1%. This also means that a stranger from the other side of the planet is only twice as different from you as is your sibling. Gathering five persons from throughout the planet produces no more variety than gathering five siblings. What is the percentage difference in genetic makeup between men and women, between members of an extended family, or between humans and chimpanzees?

    It is often mentioned that humans and chimpanzees share 98% of their genes. (You might like to view Did Humans Evolve? at http://www.pbs.org/wgbh/evolution/library/11/2/e_s_5.html.) This means that the two species differ by only about nine hundred genes, which is about 900,000 A-T, G-C base pairs. The 0.1% difference between unrelated human individuals is 5% as great as the 2% difference between humans and chimpanzees. Both being mammals, humans and mice share 85% of their genes because most genes make lungs and livers and such. We animals are not all that different from each other, we mammals are even less so, and we primates have the least differences of all. Just as mouse and human insides are much the same, their outer behaviors also differ little: we both forage, mate, raise children, and grow old. While human DNA codes for only twice as many proteins as does mouse or fly DNA, some flowers have a greater number of genes than do humans. The article Initial sequencing and comparative analysis of the mouse genome in the December, 5, 2002 Nature magazine, explains that less than 1% of the genes of a mouse occur only in mice, 14% of its genes are common only to other mammals, 6% is shared with other chordates, 27% with other metazoans, 29% shared with eurkaryotes (single-celled creatures having a nucleus), and 23% with prokaryotes that have no nucleus. The figure can be seen at www.nature.com/nature/journal/v420/n6915/fig_tab/nature01262_F17.html. (Prokaryotes existed for two billion years before eurkaryotes first appeared.) Generalizing freely to ourselves, this means that approximately the same percentages of our genes are unique to us Homo sapien sapiens and similar percentages make us mammals and chordates and such. The percentages of genes serving various functions is shown as a pie chart at www.tulane.edu/~biochem/lecture/723/humgen.html. Since the average gene-divergence rate between species is about 1% every three million years, the 15% difference in genes between mice and humans means that the two species diverged about 45 million years ago. We share 50% of our genes with those of worm.

    As mentioned in Chapter 1, the Human Genome Project studied the 3.6 billion letters in human DNA This project found that the operation of a human is conducted by thirty or forty thousand genes encoding one or two hundred thousand proteins. In contrast, bacteria typically have one to four thousand genes. The report at www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.43 explains that certain crucial, genetic information has been conserved since the Earth’s life first formed. A comparison of gene counts between species is given at http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.table.45. The table found at the website at http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.table.62 shows that about two hundred gene families are common to all three of the branches of living creatures. The three links above refer to the textbook Molecular Biology of the Cell by that can be viewed at www.garlandscience.com/textbooks/0815332181.asp or searched at www.ncbi.nlm.nih.gov/books.

    In the following chapters we will look at the development of social primates and of humans. The behavior of mammals and primates will then be discussed and compared. We will see that primates differ from the other mammals in that they have a more complicated social system. We will also see that a local climate shift in Africa promoted a change in primates that led to humans. In further chapters we will see that, in various places of the world during the times of certain combinations of population levels and climate shifts and such, more and more groups of humans turned to full-time farming. The subsequent population growth led to cities, states, and to our civilization.

    Each individual living creature develops from a parent cell, grows, and operates as its DNA steers the production of the needed proteins from absorbed and ingested light and chemicals. But that’s not the end of it. The exchange of chemical and electrical signals between cell components and between other cells gives rise to consciousness. That exchange might be consciousness. The most important brain chemicals are experienced as emotions and feelings, and they elicit behaviors. Each animal experiences, feels, and behaves. But that’s not the end of it. Many species form social systems in which there is a close interaction between the members of that species. But that’s not the end of it. Various species have parenting behaviors that forms a close relation between parent and offspring. About 5% of mammals form monogamous parenting pairs–some of these operate as nuclear families of parents and siblings. Primates cooperate as extended families of related individuals. But that’s not the end of it. Some species form culture, which consists of the recipes for how to do everything in life, that is taught from parent to offspring and becomes modified through the generations. Today, there is one species who has taken communication, culture, and tool-making to the extent that has resulted in civilization. Civilization includes government, business, organized religion, and technology and such. But that’s not the end of it. All of the Earth’s species are interrelated in predator, prey, and symbiotic manners in a web of life. Each species directly depends on many others and closely depends on all of the others. But that’s not the end of it. All species exist in the environment of inorganic chemicals and in the climate, which is driven by the sun–one of billions of stars in the galaxy, which is one of billions of stars in the universe. But that’s not the end of it.


Questions


1. What is the difference between living matter and nonliving matter?

2. Is life more than atoms and molecules?

3. Is a human more than atoms? More than an amoeba? More than a fish, a frog, a mouse, or a monkey?

4. If combinations of electrically bound atoms produce life–where "life" is self-duplicating and self-directing combinations of atoms–can combinations of particles that are bound by gravity or by the nuclear force result in life? (There are science fiction books containing these possibilities.)

5. If a robot monitors its surroundings, records its experiences, finds cause and effect patterns from its experiences, and chemically processes iron and sand and such to make copies of itself, is it then alive? If mistakes occasionally occur during the duplication process, what is the chance that they will improve the robot's operation? Would it then be evolving? What else could cause an evolution in this robot? For interviews with scientists involved in artificial intelligence, visit www.aaai.org/AITopics/html/interview.html. You might describe the points of one such interview. Visit www.aaai.org/AITopics/html/show.html for many links. For a video of Honda’s robot, visit http://world.honda.com/HDTV/ASIMO/New-ASIMO-run-6kmh/index.html.

6. How does your set of emotions compare with those of reptiles, birds, worms, or mice?

7. How are we related to chimps, whales, algae, worms, insects, and birds?

8. If people's knees bent the other way what would chairs look like?

9. Can a life form be created by designing its DNA?

10. Silicon is chemically similar to carbon. Are there any silicon-based life-forms?

11. How has it occurred that so many different animals sneeze, yawn, and close their eyes while taking a bite out of their food? Which types of animals do this and when did it begin?

12. Find an example where one species has split into two different species due to a change in the environment. Find a split that occurred as one species expanded beyond the edge of its home environment. Before this expansion occurred, were some members of that species already matched to that differing environment beyond the edge?

13. Describe the evolution of the horse or the whale.

14. For a typical species, what percentage of its genetic code becomes mutated with each generation? If the genetic code of humans and chimpanzees differs by 2%, how many generations have elapsed since they took separate paths?

15. How many chemical reactions occur per hour in your liver, your brain, and your body? How many atoms are involved in these processes? How many illnesses have been identified to be caused by genetic defects that result in incorrect chemical processes?

16. Find a case where a change in the source of food of a species led to a change in that species.

17. Find a case where a change in the predators of a species led to a change in that species.

18. Find a case where a mutation (error) caused a change in a species.

19. Which rules of nature result in life?

20. Find the range in a few human traits.

21. Describe a relationship between humans and another species.

22. Algae, bacteria, worms, and fish are very old. Why haven't they all evolved into something else?

23. Do you have any actions or behaviors that you inherited from your reptilian or amphibian ancestors? When you enjoy basking in the sun are you repeating a behavior passed down from your reptilian ancestors? Is this more than a coincidence?

24. Did the number of atoms contained in an early, developing life-form grow linearly in time? Would this number grow in proportion to its width, surface area, or volume? What is the fractal dimension of a protein? (This dimension gives an easy but approximate way to calculate growth.)

25. Does a fish taste salt water? Do we taste water or smell air? Does our inability to taste water remain from our sea-life ancestry? Why can we taste salt? Does a horse or a cow taste dirt? Since they eat the adjacent material, do monkeys sense tree limbs to be neutral, bad, or good tasting?

26. Compare the mechanical efficiency of crocodile and snake motion.

27. Create a piece of art that explains how you feel about the types and sequence of animals in the world.

28. Does DNA continually test wide extremes? Has DNA incorporated a search algorithm to find the best of 2n possible solutions in just n generations? For example, does it employ a binary search which first tests the extremities of a wide range of possibilities, then tests the midpoints of that range, and after gauging success it repeatedly cuts the remaining range in half. This would accomplish in twenty generations what an exhaustive search would take one million generations to do. The available range is continually cut in half as illustrated in the following guessing game. Think of a number between one and one-million, say 314,152. Another person, the "guesser," then asks if your number is one-half million, which is the midpoint of the available range. You answer that your number is below that guess. The guesser now knows that the answer is greater than zero but less than one-half million. This means that the search area has been cut in half. The guesser then asks is your number 250,000, which is at the midpoint of the remaining search region, and you answer it is above that number. The guesser has once again cut the search area in half and knows your number is between 250,000 and 500,000. The number will be found within twenty such guess-and-replies because a search range of one million when chopped in half twenty times results in one possible value.

29. What would you say if you looked at a drop of water in a microscope and saw a group of one hundred bacteria cells lined up to form the letters of the message “Hello”? Have aliens ever lined up our electromagnetic radiations to “spell” something that amused them though we didn’t know it had happened?

30. Are organic compounds and amino acids forming in the ocean today? Are they continually being eaten?

31. Should we humans design viruses meant to cure our diseases? Should we replace misbehaving genes with properly functioning copies.

32. Should we conduct research into altering our own genetic makeup?

33. Is a brain a generic device that would learn to operate the body of whatever species in which it finds itself? At birth, if you switched brains between two species, what would happen?


Primary sources for the chapter


     The Chemistry of Life by Martin Olomucki, 1993, McGraw-Hill New York.

     The Realm of Molecules, by Raymond Daudel, 1993, McGraw-Hill New York.

     Life Through Time, by Harold L Levin, 1975, Wm. C. Brown Company Publishers.

     Our Molecular Nature, by David S Goodsell, 1996, Springer-Verlag New York.


Suggestions for further reading


     The Sciences, An Integrated Approach, James Trefil and Robert M. Hazen, 2004, John Wiley & Sons, Inc., Hoboken, NJ. This is a one-year college course in the fundamentals of physics, astronomy, chemistry, geology, and biology.

     The Structure of Evolutionary Theory, Stephen Jay Gould, 2002, The Belknap Press of Harvard University Press, Cambridge, Massachusetts.

     The Double Helix, Edited by Gunther S Stent, 1980, W.W. Norton and Company New York. Gunther tells the story of Watson and Crick's discovery of the structure of the DNA molecule.

     The Way Life Works, Mahlon Hoagland and Bert Dodson, 1995, Times Books of Random House New York.

     The book of Life, Edited by Stephen J Gould, 1993, W.W. Norton and Company New York.

     Molecular Biology of the Cell, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, 2002, Garland Science, New York.

     Vertebrate Life, third edition, by F. Harvey Pough, John B Heiser, William N McFarland, 1989, Macmillan Publishing New York.

     The Raptor and the Lamb (Predators and Prey in the Living World), Christopher McGowen 1997, Henry Holt and Company Inc, New York.

     Prehistoric Life by David Norman, 1994 , MacMillan USA.

     From so Simple a Beginning, The Book of Evolution by Philip Whitfield, 1993, Macmillan Publishing Co, New York.

     The Vertebrate Story by Alfred Sherwood Romer, 1959, University of Chicago Press, Chicago.

     Life, Richard Fortey, 1997, Alfred A Knopf Inc, New York.

     Wonderful Life, Stephen Jay Gould, 1989, W. W. Norton & Co, New York.

     Life, A Natural History of the first Four Billion Years of Life on Earth, Richard Fortey, 1998, Alfred A Knopf, New York.

     One world, the interaction of science and theology, John Polkinhorne, 1986, Princeton University Press, Princeton, New Jersey.

     Microcosmos by Jeremy Burgess, Michael Marten, Rosemary Taylor, 1987, Cambridge University Press, Cambridge.



 

 



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