We are searching data for your request:
Upon completion, a link will appear to access the found materials.
Evolution is change in the heritable traits of biological populations over successive generations. Evolutionary processes give rise to diversity at every level of biological organization, including the levels of species, individual organisms, and molecules. In Unit 4, the core concepts of evolution are discussed in this unit with examples illustrating evolutionary processes. Additionally, the evolutionary basis of biology reappears throughout the textbook in general discussion and is reinforced through special call-out features highlighting specific evolution-based topics.
Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski (Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY 4.0; Download for free at http://cnx.org/contents/[email protected]).
Worksheet The Selection Process Biology Chapter 11 Answers
Chapter 11 section 4 meiosis worksheet answer key. Worksheets are biology 1 work i selected answers chapter 11 biology workbook answers prentice hall biology chapter 11 assessment answer key chapter 1 what is biology work chapter 11 the principles of ecology work glencoe science chapter resources answers for support work chapter 8 biology eoc study guide answer key and content focus report.
Key To Selection Pressures Worksheet Date Period Worksheet The
Once you find your worksheet.
Worksheet the selection process biology chapter 11 answers. Chapter 11 biology workbook answerspdf free pdf download. Advanced placement unit 4. Video worksheet was darwin right or wrong.
C h a p t e r 1 1 directions. The smallest unit of evolution concept 231. Chapter 11 biology workbook answerspdf free pdf download now.
Chapter 12 review game. 324 chapter 11 lesson 4. For each of the three scenarios below identify which type of selection would occur and explain your reasoning.
Some of the worksheets displayed are chapter 11 the principles of ecology work chapter 1 the science of biology summary biology eoc study guide with practice questions biology 1 work i selected answers answer key chapter 16 plant biology work section review 11 2 enrichment. Answer the following questions using your notes and textbook chapters 11. The selection process b i o l o g y.
Some of the worksheets displayed are chapter 1 what is biology work biology 1 work i selected answers prentice hall biology chapter 11 assessment answer key ap biology test 3 ap biology chapters 1 work science 9th biology crossword name chapter 11 the principles of ecology work. The selection process b i o l o g y. Name date period worksheet.
The hardy weinberg equation can be used to test whether a population is evolving concept 233. For each of the three scenarios below identify which type of selection would occur and explain your reasoning. A fishy twist on adaptations.
The selection process biology. Chapter 11 review game. Biology chapter 11 answer key.
Mechanisms of evolution chapter 23. Each organism must inherit a single copy of every gene from each of its parents gametes are formed by a process that separates. Tricias compilation for answer sheet for chapter 11 dna and genes worksheet biology student reader workbook unit 5 ecology.
C h a p t e r 1 1 directions. Build a beast lab. Chapter 11 biology answer sheet.
Mutation and sexual reproduction produce the genetic variation that makes evolution possible concept 232. Section 114 meiosis. Showing top 8 worksheets in the category chapter 11 biology answer sheet.
The evolution of populations overview. Figure 1115 during crossing over the alleles. For each of the three scenarios below identify which type of selection would occur and explain your reasoning.
In thegraph provided illustrate the type of selection and the change in distribution of traits that would occur within each population. Answer the following questions using your notes and textbook chapters 11. Chapter 10 review game.
Ecology worksheets and handouts. Answer the following questions using your notes and textbook chapters 11.
Summary Book Selling Today Partnering To Create Value Studocu
Pdf Chapter 11 Experimental Research
Openstax Biology Ch19 The Evolution Of Populations Top Hat
Fillable Online Losalusd K12 Ca Worksheet The Selection Process Ch
The Selection Process Worksheet Natural Selection Phenotypic Trait
Directional Selection Stabilizing Directional And Disruptive Selection
Genetics Study Guide Worksheets Teachers Pay Teachers
Natural Selection Bioninja
Kendriya Vidyalaya Tirumalagiri
Free Biology Textbook Available For Download Openstax
Simbio Virtual Biology Labs And Chapters Evolution Simbio
Embryo Selection For Intelligence Gwern Net
Important Questions For Cbse Class 12 Biology Chapter 5 Principles
Key To Selection Pressures Worksheet Date Period Worksheet The
Pdf Elephant Population Biology And Ecology
Ncert Exemplar Class 12 Biology Chapter 5 Principles Of Inheritance
Quiz Worksheet Darwin S Theory Of Natural Selection Study Com
Power Notes Answer Key Section 1 1 Section 1 2 Section 1 3
Levels Of Organization In Biology Stanford Encyclopedia Of Philosophy
Modern Biology Chapter Tests With Answer Key General And Advanced Pdf
Directional Selection Wikipedia
Practical Chapter 11 2 Test Bank Questions Answers Psy1101
Gre Biology Practice Test
Worksheet The Selection Process Ch 11 2011 Pdf Name Date Period
The Selection Process Worksheet Natural Selection Phenotypic Trait
The Theory Of Evolution And Natural Selection Crossword Wordmint
Natural Selection Vs Evolution Answers In Genesis
Adaptive Evolution Boundless Biology
Introduction To Evolution And Natural Selection Video Khan Academy
Adams Amelia Honors And Academic Biology Resources
"Biology" derives from the Ancient Greek words of βίος romanized bíos meaning "life" and -λογία romanized logía (-logy) meaning "branch of study" or "to speak".   Those combined make the Greek word βιολογία romanized biología meaning biology. Despite this, the term βιολογία as a whole didn't exist in Ancient Greek. The first to borrow it was the English and French (biologie). Historically there was another term for "biology" in English, lifelore it is rarely used today.
The Latin-language form of the term first appeared in 1736 when Swedish scientist Carl Linnaeus (Carl von Linné) used biologi in his Bibliotheca Botanica. It was used again in 1766 in a work entitled Philosophiae naturalis sive physicae: tomus III, continens geologian, biologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff. The first German use, Biologie, was in a 1771 translation of Linnaeus' work. In 1797, Theodor Georg August Roose used the term in the preface of a book, Grundzüge der Lehre van der Lebenskraft. Karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological, physiological and psychological perspective (Propädeutik zum Studien der gesammten Heilkunst). The term came into its modern usage with the six-volume treatise Biologie, oder Philosophie der lebenden Natur (1802–22) by Gottfried Reinhold Treviranus, who announced: 
The objects of our research will be the different forms and manifestations of life, the conditions and laws under which these phenomena occur, and the causes through which they have been affected. The science that concerns itself with these objects we will indicate by the name biology [Biologie] or the doctrine of life [Lebenslehre].
The earliest of roots of science, which included medicine, can be traced to ancient Egypt and Mesopotamia in around 3000 to 1200 BCE.   Their contributions later entered and shaped Greek natural philosophy of classical antiquity.     Ancient Greek philosophers such as Aristotle (384–322 BCE) contributed extensively to the development of biological knowledge. His works such as History of Animals were especially important because they revealed his naturalist leanings, and later more empirical works that focused on biological causation and the diversity of life. Aristotle's successor at the Lyceum, Theophrastus, wrote a series of books on botany that survived as the most important contribution of antiquity to the plant sciences, even into the Middle Ages. 
Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dīnawarī (828–896), who wrote on botany,  and Rhazes (865–925) who wrote on anatomy and physiology. Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought, especially in upholding a fixed hierarchy of life.
Biology began to quickly develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining. 
Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell. Then, in 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most biologists accepted all three tenets of what came to be known as cell theory.  
Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735 (variations of which have been in use ever since), and in the 1750s introduced scientific names for all his species.  Georges-Louis Leclerc, Comte de Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility of common descent. Although he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought his work influenced the evolutionary theories of both Lamarck and Darwin. 
Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck, who was the first to present a coherent theory of evolution.  He posited that evolution was the result of environmental stress on properties of animals, meaning that the more frequently and rigorously an organ was used, the more complex and efficient it would become, thus adapting the animal to its environment. Lamarck believed that these acquired traits could then be passed on to the animal's offspring, who would further develop and perfect them.  However, it was the British naturalist Charles Darwin, combining the biogeographical approach of Humboldt, the uniformitarian geology of Lyell, Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, who forged a more successful evolutionary theory based on natural selection similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions.   Darwin's theory of evolution by natural selection quickly spread through the scientific community and soon became a central axiom of the rapidly developing science of biology.
The basis for modern genetics began with the work of Gregor Mendel, who presented his paper, "Versuche über Pflanzenhybriden" ("Experiments on Plant Hybridization"), in 1865,  which outlined the principles of biological inheritance, serving as the basis for modern genetics.  However, the significance of his work was not realized until the early 20th century when evolution became a unified theory as the modern synthesis reconciled Darwinian evolution with classical genetics.  In the 1940s and early 1950s, a series of experiments by Alfred Hershey and Martha Chase pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes. A focus on new kinds of model organisms such as viruses and bacteria, along with the discovery of the double-helical structure of DNA by James Watson and Francis Crick in 1953, marked the transition to the era of molecular genetics. From the 1950s to the present times, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons. Finally, the Human Genome Project was launched in 1990 with the goal of mapping the general human genome. This project was essentially completed in 2003,  with further analysis still being published. The Human Genome Project was the first step in a globalized effort to incorporate accumulated knowledge of biology into a functional, molecular definition of the human body and the bodies of other organisms.
Atoms and molecules
All living organisms are made up of matter and all matter is made up of elements.  Oxygen, carbon, hydrogen, and nitrogen are the four elements that account for 96% of all living organisms, with calcium, phosphorus, sulfur, sodium, chlorine, and magnesium accounting for the remaining 3.7%.  Different elements can combine to form compounds such as water, which is fundamental to life.  Life on Earth began from water and remained there for about three billions years prior to migrating onto land.  Matter can exist in different states as a solid, liquid, or gas.
The smallest unit of an element is an atom, which is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Individual atoms can be held together by chemical bonds to form molecules and ionic compounds.  Common types of chemical bonds include ionic bonds, covalent bonds, and hydrogen bonds. Ionic bonding involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities,  and is the primary interaction occurring in ionic compounds. Ions are atoms (or groups of atoms) with an electrostatic charge. Atoms that gain electrons make negatively charged ions (called anions) whereas those that lose electrons make positively charged ions (called cations).
Unlike ionic bonds, a covalent bond involves the sharing of electron pairs between atoms. These electron pairs and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. 
A hydrogen bond is primarily an electrostatic force of attraction between a hydrogen atom which is covalently bound to a more electronegative atom or group such as oxygen. A ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them. When more molecules are present, as is the case with liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with a hydrogen on another water molecule.
With the exception of water, nearly all the molecules that make up each living organism contain carbon.   Carbon can form very long chains of interconnecting carbon–carbon bonds, which are strong and stable. The simplest form of an organic molecule is the hydrocarbon, which is a large family of organic compounds that are composed of hydrogen atoms bonded to a chain of carbon atoms. A hydrocarbon backbone can be substituted by other atoms. When combined with other elements such as oxygen, hydrogen, phosphorus, and sulfur, carbon can form many groups of important biological compounds such as sugars, fats, amino acids, and nucleotides.
Molecules such as sugars, amino acids, and nucleotides can act as single repeating units called monomers to form chain-like molecules called polymers via a chemical process called condensation.  For example, amino acids can form polypeptides whereas nucleotides can form strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Polymers make up three of the four macromolecules (polysaccharides, lipids, proteins, and nucleic acids) that are found in all living organisms. Each macromolecule plays a specialized role within any given cell. Some polysaccharides, for instance, can function as storage material that can be hydrolyzed to provide cells with sugar. Lipids are the only class of macromolecules that are not made up of polymers and the most biologically important lipids are fats, phospholipids, and steroids.  Proteins are the most diverse of the macromolecules, which include enzymes, transport proteins, large signaling molecules, antibodies, and structural proteins. Finally, nucleic acids store, transmit, and express hereditary information. 
Cell theory states that cells are the fundamental units of life, that all living things are composed of one or more cells, and that all cells arise from preexisting cells through cell division.  Most cells are very small, with diameters ranging from 1 to 100 micrometers and are therefore only visible under a light or electron microscope.  There are generally two types of cells: eukaryotic cells, which contain a nucleus, and prokaryotic cells, which do not. Prokaryotes are single-celled organisms such as bacteria, whereas eukaryotes can be single-celled or multicellular. In multicellular organisms, every cell in the organism's body is derived ultimately from a single cell in a fertilized egg.
Every cell is enclosed within a cell membrane that separates its cytoplasm from the extracellular space.  A cell membrane consists of a lipid bilayer, including cholesterols that sit between phospholipids to maintain their fluidity at various temperatures. Cell membranes are semipermeable, allowing small molecules such as oxygen, carbon dioxide, and water to pass through while restricting the movement of larger molecules and charged particles such as ions.  Cell membranes also contains membrane proteins, including integral membrane proteins that go across the membrane serving as membrane transporters, and peripheral proteins that loosely attach to the outer side of the cell membrane, acting as enzymes shaping the cell.  Cell membranes are involved in various cellular processes such as cell adhesion, storing electrical energy, and cell signalling and serve as the attachment surface for several extracellular structures such as a cell wall, glycocalyx, and cytoskeleton.
Within the cytoplasm of a cell, there are many biomolecules such as proteins and nucleic acids.  In addition to biomolecules, eukaryotic cells have specialized structures called organelles that have their own lipid bilayers or are spatially units. These organelles include the cell nucleus, which contains a cell's genetic information, or mitochondria, which generates adenosine triphosphate (ATP) to power cellular processes. Other organelles such as endoplasmic reticulum and Golgi apparatus play a role in the synthesis and packaging of proteins, respectively. Biomolecules such as proteins can be engulfed by lysosomes, another specialized organelle. Plant cells have additional organelles that distinguish them from animal cells such as a cell wall, chloroplasts, and vacuole.
All cells require energy to sustain cellular processes. Energy is the capacity to do work, which, in thermodynamics, can be calculated using Gibbs free energy. According to the first law of thermodynamics, energy is conserved, i.e., cannot be created or destroyed. Hence, chemical reactions in a cell do not create new energy but are involved instead in the transformation and transfer of energy.  Nevertheless, all energy transfers lead to some loss of usable energy, which increases entropy (or state of disorder) as stated by the second law of thermodynamics. As a result, living organisms such as cells require continuous input of energy to maintain a low state of entropy. In cells, energy can be transferred as electrons during redox (reduction–oxidation) reactions, stored in covalent bonds, and generated by the movement of ions (e.g., hydrogen, sodium, potassium) across a membrane.
Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration) or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts – they allow a reaction to proceed more rapidly without being consumed by it – by reducing the amount of activation energy needed to convert reactants into products. Enzymes also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.
Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products.  The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy because weak high-energy bonds, in particular in molecular oxygen,  are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. The overall reaction occurs in a series of biochemical steps, some of which are redox reactions. Although cellular respiration is technically a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow, controlled release of energy from the series of reactions.
Sugar in the form of glucose is the main nutrient used by animal and plant cells in respiration. Cellular respiration involving oxygen is called aerobic respiration, which has four stages: glycolysis, citric acid cycle (or Krebs cycle), electron transport chain, and oxidative phosphorylation.  Glycolysis is a metabolic process that occurs in the cytoplasm whereby glucose is converted into two pyruvates, with two net molecules of ATP being produced at the same time.  Each pyruvate is then oxidized into acetyl-CoA by the pyruvate dehydrogenase complex, which also generates NADH and carbon dioxide. Acetyl-Coa enters the citric acid cycle, which takes places inside the mitochondrial matrix. At the end of the cycle, the total yield from 1 glucose (or 2 pyruvates) is 6 NADH, 2 FADH2, and 2 ATP molecules. Finally, the next stage is oxidative phosphorylation, which in eukaryotes, occurs in the mitochondrial cristae. Oxidative phosphorylation comprises the electron transport chain, which is a series of four protein complexes that transfer electrons from one complex to another, thereby releasing energy from NADH and FADH2 that is coupled to the pumping of protons (hydrogen ions) across the inner mitochondrial membrane (chemiosmosis), which generates a proton motive force.  Energy from the proton motive force drives the enzyme ATP synthase to synthesize more ATPs by phosphorylating ADPs. The transfer of electrons terminates with molecular oxygen being the final electron acceptor.
If oxygen were not present, pyruvate would not be metabolized by cellular respiration but undergoes a process of fermentation. The pyruvate is not transported into the mitochondrion but remains in the cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the electron carriers so that they can perform glycolysis again and removing the excess pyruvate. Fermentation oxidizes NADH to NAD + so it can be re-used in glycolysis. In the absence of oxygen, fermentation prevents the buildup of NADH in the cytoplasm and provides NAD + for glycolysis. This waste product varies depending on the organism. In skeletal muscles, the waste product is lactic acid. This type of fermentation is called lactic acid fermentation. In strenuous exercise, when energy demands exceed energy supply, the respiratory chain cannot process all of the hydrogen atoms joined by NADH. During anaerobic glycolysis, NAD + regenerates when pairs of hydrogen combine with pyruvate to form lactate. Lactate formation is catalyzed by lactate dehydrogenase in a reversible reaction. Lactate can also be used as an indirect precursor for liver glycogen. During recovery, when oxygen becomes available, NAD + attaches to hydrogen from lactate to form ATP. In yeast, the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation. The ATP generated in this process is made by substrate-level phosphorylation, which does not require oxygen.
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organism's metabolic activities via cellular respiration. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water.    In most cases, oxygen is also released as a waste product. Most plants, algae, and cyanobacteria perform photosynthesis, which is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. 
Photosynthesis has four stages: Light absorption, electron transport, ATP synthesis, and carbon fixation.  Light absorption is the initial step of photosynthesis whereby light energy is absorbed by chlorophyll pigments attached to proteins in the thylakoid membranes. The absorbed light energy is used to remove electrons from a donor (water) to a primary electron acceptor, a quinone designated as Q. In the second stage, electrons move from the quinone primary electron acceptor through a series of electron carriers until they reach a final electron acceptor, which is usually the oxidized form of NADP + , which is reduced to NADPH, a process that takes place in a protein complex called photosystem I (PSI). The transport of electrons is coupled to the movement of protons (or hydrogen) from the stroma to the thylakoid membrane, which forms a pH gradient across the membrane as hydrogen becomes more concentrated in the lumen than in the stroma. This is analogous to the proton-motive force generated across the inner mitochondrial membrane in aerobic respiration. 
During the third stage of photosynthesis, the movement of protons down their concentration gradients from the thylakoid lumen to the stroma through the ATP synthase is coupled to the synthesis of ATP by that same ATP synthase.  The NADPH and ATPs generated by the light-dependent reactions in the second and third stages, respectively, provide the energy and electrons to drive the synthesis of glucose by fixing atmospheric carbon dioxide into existing organic carbon compounds, such as ribulose bisphosphate (RuBP) in a sequence of light-independent (or dark) reactions called the Calvin cycle. 
Cell communication (or signaling) is the ability of cells to receive, process, and transmit signals with its environment and with itself.   Signals can be non-chemical such as light, electrical impulses, and heat, or chemical signals (or ligands) that interact with receptors, which can be found embedded in the cell membrane of another cell or located deep inside a cell.   There are generally four types of chemical signals: autocrine, paracrine, juxtacrine, and hormones.  In autocrine signaling, the ligand affects the same cell that releases it. Tumor cells, for example, can reproduce uncontrollably because they release signals that initiate their own self-division. In paracrine signaling, the ligand diffuses to nearby cells and affect them. For example, brain cells called neurons release ligands called neurotransmitters that diffuse across a synaptic cleft to bind with a receptor on an adjacent cell such as another neuron or muscle cell. In juxtacrine signaling, there is direct contact between the signaling and responding cells. Finally, hormones are ligands that travel through the circulatory systems of animals or vascular systems of plants to reach their target cells. Once a ligand binds with a receptor, it can influence the behavior of another cell, depending on the type of receptor. For instance, neurotransmitters that bind with an inotropic receptor can alter the excitability of a target cell. Other types of receptors include protein kinase receptors (e.g., receptor for the hormone insulin) and G protein-coupled receptors. Activation of G protein-coupled receptors can initiate second messenger cascades. The process by which a chemical or physical signal is transmitted through a cell as a series of molecular events is called signal transduction
The cell cycle is a series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA and some of its organelles, and the subsequent partitioning of its cytoplasm into two daughter cells in a process called cell division.  In eukaryotes (i.e., animal, plant, fungal, and protist cells), there are two distinct types of cell division: mitosis and meiosis.  Mitosis is part of the cell cycle, in which replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which the total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA is replicated) and is often followed by telophase and cytokinesis which divides the cytoplasm, organelles and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of mitosis all together define the mitotic phase of an animal cell cycle—the division of the mother cell into two genetically identical daughter cells.  The cell cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed. After cell division, each of the daughter cells begin the interphase of a new cycle. In contrast to mitosis, meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions.  Homologous chromosomes are separated in the first division (meiosis I), and sister chromatids are separated in the second division (meiosis II). Both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in the last eukaryotic common ancestor.
Prokaryotes (i.e., archaea and bacteria) can also undergo cell division (or binary fission). Unlike the processes of mitosis and meiosis in eukaryotes, binary fission takes in prokaryotes takes place without the formation of a spindle apparatus on the cell. Before binary fission, DNA in the bacterium is tightly coiled. After it has uncoiled and duplicated, it is pulled to the separate poles of the bacterium as it increases the size to prepare for splitting. Growth of a new cell wall begins to separate the bacterium (triggered by FtsZ polymerization and "Z-ring" formation)  The new cell wall (septum) fully develops, resulting in the complete split of the bacterium. The new daughter cells have tightly coiled DNA rods, ribosomes, and plasmids.
Genetics is the scientific study of inheritance.    Mendelian inheritance, specifically, is the process by which genes and traits are passed on from parents to offspring.  It was formulated by Gregor Mendel, based on his work with pea plants in the mid-nineteenth century. Mendel established several principles of inheritance. The first is that genetic characteristics, which are now called alleles, are discrete and have alternate forms (e.g., purple vs. white or tall vs. dwarf), each inherited from one of two parents. Based on his law of dominance and uniformity, which states that some alleles are dominant while others are recessive an organism with at least one dominant allele will display the phenotype of that dominant allele.  Exceptions to this rule include penetrance and expressivity.  Mendel noted that during gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene, which is stated by his law of segregation. Heterozygotic individuals produce gametes with an equal frequency of two alleles. Finally, Mendel formulated the law of independent assortment, which states that genes of different traits can segregate independently during the formation of gametes, i.e., genes are unlinked. An exception to this rule would include traits that are sex-linked. Test crosses can be performed to experimentally determine the underlying genotype of an organism with a dominant phenotype.  A Punnett square can be used to predict the results of a test cross. The chromosome theory of inheritance, which states that genes are found on chromosomes, was supported by Thomas Morgans's experiments with fruit flies, which established the sex linkage between eye color and sex in these insects.  In humans and other mammals (e.g., dogs), it is not feasible or practical to conduct test cross experiments. Instead, pedigrees, which are genetic representations of family trees,  are used instead to trace the inheritance of a specific trait or disease through multiple generations. 
Deoxyribonucleic acid (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic hereditary information. The two DNA strands are known as polynucleotides as they are composed of monomers called nucleotides.   Each nucleotide is composed of one of four nitrogenous bases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. It is the sequence of these four bases along the backbone that encodes genetic information. Bases of the two polynucleotide strands are bound together by hydrogen bonds, according to base pairing rules (A with T and C with G), to make double-stranded DNA. The bases are divided into two groups: pyrimidines and purines. In DNA, the pyrimidines are thymine and cytosine whereas the purines are adenine and guanine. The two strands of DNA run in opposite directions to each other and are thus antiparallel. DNA is replicated once the two strands separate.
A gene is a unit of heredity that corresponds to a region of DNA that influences the form or function of an organism in specific ways. DNA is found as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as a cell's genome. In eukaryotes, genomic DNA is localized in the cell nucleus, or with small amounts in mitochondria and chloroplasts.  In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.  The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype.  Genes encode the information needed by cells for the synthesis of proteins, which in turn play a central role in influencing the final phenotype of the organism.
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The process is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958.    Gene expression is the most fundamental level at which a genotype gives rise to a phenotype, i.e., observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the synthesis of proteins that control an organism's structure and development, or that act as enzymes catalyzing specific metabolic pathways. A large part of DNA (e.g., >98% in humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences. Messenger RNA (mRNA) strands are created using DNA strands as a template in a process called transcription, where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U).  Under the genetic code, these mRNA strands specify the sequence of amino acids within proteins in a process called translation, which occurs in ribosomes. This process is used by all life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. Gene products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA.   All steps in the gene expression process can be regulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Regulation of gene expression gives control over the timing, location, and amount of a given gene product (protein or ncRNA) present in a cell and can have a profound effect on cellular structure and function.
A genome is an organism's complete set of DNA, including all of its genes.  Sequencing and analysis of genomes can be done using high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.    Many genes encode more than one protein, with posttranslational modifications increasing the diversity of proteins within a cell. A cell's proteome is its entire set of proteins expressed by its genome.  The genomes of prokaryotes are small, compact, and diverse. In contrast, the genomes of eukaryotes are larger and more complex such as having more regulatory sequences and much of its genome are made up of non-coding DNA sequences for functional RNA (rRNA, tRNA, and mRNA) or regulatory sequences. The genomes of various model organisms such as arabidopsis, fruit fly, mice, nematodes, and yeast have been sequenced. The sequencing of the entire human genome has yielded practical applications such as DNA fingerprinting, which can be used for paternity testing and forensics. In medicine, sequencing of the entire human genome has allowed for the identification mutations that cause tumors as well as genes that cause a specific genetic disorder. 
Biotechnology is the use of cells or living organisms to develop products for humans.  It includes tools such as recombinant DNA, which are DNA molecules formed by laboratory methods of genetic recombination such as molecular cloning, which bring together genetic material from multiple sources, creating sequences that would otherwise not be found in a genome. Other tools include the use of genomic libraries, DNA microarrays, expression vectors, synthetic genomics, and CRISPR gene editing.   Many of these tools have wide applications such as creating medically useful proteins, or improving plant cultivation and animal husbandry.  Human insulin, for example, was the first medicine to be made using recombinant DNA technology. Other approaches such as pharming can produce large quantities of medically useful products through the use of genetically modified organisms. 
Genes, development, and evolution
Development is the process by which a multicellular organism (plant or animal) goes through a series of a changes, starting from a single cell, and taking on various forms that are characteristic of its life cycle.  There are four key processes that underlie development: Determination, differentiation, morphogenesis, and growth. Determination sets the developmental fate of a cell, which becomes more restrictive during development. Differentiation is the process by which specialized cells from less specialized cells such as stem cells.   Stem cells are undifferentiated or partially differentiated cells that can differentiate into various types of cells and proliferate indefinitely to produce more of the same stem cell.  Cellular differentiation dramatically changes a cell's size, shape, membrane potential, metabolic activity, and responsiveness to signals, which are largely due to highly controlled modifications in gene expression and epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself.  Thus, different cells can have very different physical characteristics despite having the same genome. Morphogenesis, or development of body form, is the result of spatial differences in gene expression.  Specially, the organization of differentiated tissues into specific structures such as arms or wings, which is known as pattern formation, is governed by morphogens, signaling molecules that move from one group of cells to surrounding cells, creating a morphogen gradient as described by the French flag model. Apoptosis, or programmed cell death, also occurs during morphogenesis, such as the death of cells between digits in human embryonic development, which frees up individual fingers and toes. Expression of transcription factor genes can determine organ placement in a plant and a cascade of transcription factors themselves can establish body segmentation in a fruit fly. 
A small fraction of the genes in an organism's genome called the developmental-genetic toolkit control the development of that organism. These toolkit genes are highly conserved among phyla, meaning that they are ancient and very similar in widely separated groups of animals. Differences in deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts. Among the most important toolkit genes are the Hox genes. Hox genes determine where repeating parts, such as the many vertebrae of snakes, will grow in a developing embryo or larva.  Variations in the toolkit may have produced a large part of the morphological evolution of animals. The toolkit can drive evolution in two ways. A toolkit gene can be expressed in a different pattern, as when the beak of Darwin's large ground-finch was enlarged by the BMP gene,  or when snakes lost their legs as Distal-less (Dlx) genes became under-expressed or not expressed at all in the places where other reptiles continued to form their limbs.  Or, a toolkit gene can acquire a new function, as seen in the many functions of that same gene, distal-less, which controls such diverse structures as the mandible in vertebrates,   legs and antennae in the fruit fly,  and eyespot pattern in butterfly wings.  Given that small changes in toolbox genes can cause significant changes in body structures, they have often enabled convergent or parallel evolution.
A central organizing concept in biology is that life changes and develops through evolution, which is the change in heritable characteristics of populations over successive generations.   Evolution is now used to explain the great variations of life on Earth. The term evolution was introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809,  and fifty years later Charles Darwin and Alfred Russel Wallace formulated the theory of evolution by natural selection.     According to this theory, individuals differ from each other with respect to their heritable traits, resulting in different rates of survival and reproduction. As a results, traits that are better adapted to their environment are more likely to be passed on to subsequent generations.   Darwin was not aware of Mendel's work of inheritance and so the exact mechanism of inheritance that underlie natural selection was not well-understood  until the early 20th century when the modern synthesis reconciled Darwinian evolution with classical genetics, which established a neo-Darwinian perspective of evolution by natural selection.  This perspective holds that evolution occurs when there are changes in the allele frequencies within a population of interbreeding organisms. In the absence of any evolutionary process acting on a large random mating population, the allele frequencies will remain constant across generations as described by the Hardy–Weinberg principle. 
Another process that drives evolution is genetic drift, which is the random fluctuations of allele frequencies within a population from one generation to the next.  When selective forces are absent or relatively weak, allele frequencies are equally likely to drift upward or downward at each successive generation because the alleles are subject to sampling error.  This drift halts when an allele eventually becomes fixed, either by disappearing from the population or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone.
Speciation is the process of splitting one lineage into two lineages that evolve independently from each other.  For speciation to occur, there has to be reproductive isolation.  Reproductive isolation can result from incompatibilities between genes as described by Bateson–Dobzhansky–Muller model. Reproductive isolation also tends to increase with genetic divergence. Speciation can occur when there are physical barriers that divide an ancestral species, a process known as allopatric speciation.  In contrast, sympatric speciation occurs in the absence of physical barriers.
Pre-zygotic isolation such as mechanical, temporal, behavioral, habitat, and gametic isolations can prevent different species from hybridizing.  Similarly, post-zygotic isolations can result in hybridization being selected against due to the lower viability of hybrids or hybrid infertility (e.g., mule). Hybrid zones can emerge if there were to be incomplete reproductive isolation between two closely related species.
A phylogeny is an evolutionary history of a specific group of organisms or their genes.  A phylogeny can be represented using a phylogenetic tree, which is a diagram showing lines of descent among organisms or their genes. Each line drawn on the time axis of a tree represents a lineage of descendents of a particular species or population. When a lineage divides into two, it is represented as a node (or split) on the phylogenetic tree. The more splits there are over time, the more branches there will be on the tree, with the common ancestor of all the organisms in that tree being represented by the root of that tree. Phylogenetic trees may portray the evolutionary history of all life forms, a major evolutionary group (e.g., insects), or an even smaller group of closely related species. Within a tree, any group of species designated by a name is a taxon (e.g., humans, primates, mammals, or vertebrates) and a taxon that consists of all its evolutionary descendants is a clade. Closely related species are referred to as sister species and closely related clades are sister clades.
Phylogenetic trees are the basis for comparing and grouping different species.  Different species that share a feature inherited from a common ancestor are described as having homologous features. Homologous features may be any heritable traits such as DNA sequence, protein structures, anatomical features, and behavior patterns. A vertebral column is an example of a homologous feature shared by all vertebrate animals. Traits that have a similar form or function but were not derived from a common ancestor are described as analogous features. Phylogenies can be reconstructed for a group of organisms of primary interests, which are called the ingroup. A species or group that is closely related to the ingroup but is phylogenetically outside of it is called the outgroup, which serves a reference point in the tree. The root of the tree is located between the ingroup and the outgroup.  When phylogenetic trees are reconstructed, multiple trees with different evolutionary histories can be generated. Based on the principle of Parsimony (or Occam's razor), the tree that is favored is the one with the fewest evolutionary changes needed to be assumed over all traits in all groups. Computational algorithms can be used to determine how a tree might have evolved given the evidence. 
Phylogeny provides the basis of biological classification, which is based on Linnaean taxonomy that was developed by Carl Linnaeus in the 18th century.  This classification system is rank-based, with the highest rank being the domain followed by kingdom, phylum, class, order, family, genus, and species.  All living organisms can be classified as belonging to one of three domains: Archaea (originally Archaebacteria) bacteria (originally eubacteria), or eukarya (includes the protist, fungi, plant, and animal kingdoms).  A binomial nomenclature is used to classify different species. Based on this system, each species is given two names, one for its genus and another for its species.  For example, humans are Homo sapiens, with Homo being the genus and sapiens being the species. By convention, the scientific names of organisms are italicized, with only the first letter of the genus capitalized.  
History of life
The history of life on Earth traces the processes by which organisms have evolved from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago and all life on Earth, both living and extinct, descended from a last universal common ancestor that lived about 3.5 billion years ago.   The similarities among all known present-day species indicate that they have diverged through the process of evolution from their common ancestor.  Biologists regard the ubiquity of the genetic code as evidence of universal common descent for all bacteria, archaea, and eukaryotes.    
Microbal mats of coexisting bacteria and archaea were the dominant form of life in the early Archean Epoch and many of the major steps in early evolution are thought to have taken place in this environment.  The earliest evidence of eukaryotes dates from 1.85 billion years ago,   and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism. Later, around 1.7 billion years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions. 
Algae-like multicellular land plants are dated back even to about 1 billion years ago,  although evidence suggests that microorganisms formed the earliest terrestrial ecosystems, at least 2.7 billion years ago.  Microorganisms are thought to have paved the way for the inception of land plants in the Ordovician period. Land plants were so successful that they are thought to have contributed to the Late Devonian extinction event. 
Ediacara biota appear during the Ediacaran period,  while vertebrates, along with most other modern phyla originated about 525 million years ago during the Cambrian explosion.  During the Permian period, synapsids, including the ancestors of mammals, dominated the land,  but most of this group became extinct in the Permian–Triassic extinction event 252 million years ago.  During the recovery from this catastrophe, archosaurs became the most abundant land vertebrates  one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods.  After the Cretaceous–Paleogene extinction event 66 million years ago killed off the non-avian dinosaurs,  mammals increased rapidly in size and diversity.  Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify. 
Bacteria and Archaea
Bacteria are a type of cell that constitute a large domain of prokaryotic microorganisms. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste,  and the deep biosphere of the earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory. 
Archaea constitute the other domain of prokaryotic cells and were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), a term that has fallen out of use.  Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi.  Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes,  including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding unlike bacteria, no known species of Archaea form endospores.
The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.
Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut, mouth, and on the skin.  Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation nitrogen cycling organic compound turnover and maintaining microbial symbiotic and syntrophic communities, for example. 
Protists are eukaryotic organism that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor),  the exclusion of other eukaryotes means that protists do not form a natural group, or clade. [a] So some protists may be more closely related to animals, plants, or fungi than they are to other protists however, like algae, invertebrates, or protozoans, the grouping is used for convenience. 
The taxonomy of protists is still changing. Newer classifications attempt to present monophyletic groups based on morphological (especially ultrastructural),    biochemical (chemotaxonomy)   and DNA sequence (molecular research) information.   Because protists as a whole are paraphyletic, new systems often split up or abandon the kingdom, instead treating the protist groups as separate lines of eukaryotes.
Plants are mainly multicellular organisms, predominantly photosynthetic eukaryotes of the kingdom Plantae. Botany is the study of plant life, which would exclude fungi and some algae. Botanists have studied approximately 410,000 species of land plants of which some 391,000 species are vascular plants (including approximately 369,000 species of flowering plants),  and approximately 20,000 are bryophytes. 
Algae is a large and diverse group of photosynthetic eukaryotic organisms. Included organisms range from unicellular microalgae, such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga. Most are aquatic and autotrophic and lack many of the distinct cell and tissue types, such as stomata, xylem and phloem, which are found in land plants. The largest and most complex marine algae are called seaweeds, while the most complex freshwater forms are the Charophyta.
Nonvascular plants are plants without a vascular system consisting of xylem and phloem. Instead, they may possess simpler tissues that have specialized functions for the internal transport of water. Vascular plants, on the other hand, are a large group of plants (c. 300,000 accepted known species)  that are defined as land plants with lignified tissues (the xylem) for conducting water and minerals throughout the plant.  They also have a specialized non-lignified tissue (the phloem) to conduct products of photosynthesis. Vascular plants include the clubmosses, horsetails, ferns, gymnosperms (including conifers) and angiosperms (flowering plants).
Seed plants (or spermatophyte) comprise five divisions, four of which are grouped as gymnosperms and one is angiosperms. Gymnosperms includes conifers, cycads, Ginkgo, and gnetophytes. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or solitary as in yew, Torreya, Ginkgo.  Angiosperms are the most diverse group of land plants, with 64 orders, 416 families, approximately 13,000 known genera and 300,000 known species.  Like gymnosperms, angiosperms are seed-producing plants. They are distinguished from gymnosperms by having characteristics such as flowers, endosperm within their seeds, and production of fruits that contain the seeds.
Fungi are eukaryotic organisms that include microorganisms such as yeasts and molds, as well as the more familiar mushrooms. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), which share a common ancestor (from a monophyletic group). This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds).
Most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment.
The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species.  Of these, only about 148,000 have been described,  with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. 
Animals are multicellular eukaryotic organisms that form the kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs.
Sponges, the members of the phylum Porifera, are a basal Metazoa (animal) clade as a sister of the Diploblasts.      They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through them, consisting of jelly-like mesohyl sandwiched between two thin layers of cells.
97%) of animal species are invertebrates,  which are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snail, bivalves, squids, and octopuses), annelid (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals). Many invertebrate taxa have a greater number and variety of species than the entire subphylum of Vertebrata. 
In contrast, vertebrates comprise all species of animals within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,963 species described.  Vertebrates include such groups as jawless fishes, jawed vertebrates such as cartilaginous fishes (sharks, rays, and ratfish), bony fishes, tetrapods such as amphibians, reptiles, birds and mammals.
Viruses are submicroscopic infectious agents that replicate inside the living cells of organisms.  Viruses infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.   More than 6,000 virus species have been described in detail.  Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity.  
When infected, a host cell is forced to rapidly produce thousands of identical copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions, consisting of the genetic material (DNA or RNA), a protein coat called capsid, and in some cases an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope, as they are one-hundredth the size of most bacteria.
The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction.  Because viruses possess some but not all characteristics of life, they have been described as "organisms at the edge of life",  and as self-replicators. 
Viruses can spread in many ways. One transmission pathway is through disease-bearing organisms known as vectors: for example, viruses are often transmitted from plant to plant by insects that feed on plant sap, such as aphids and viruses in animals can be carried by blood-sucking insects. Influenza viruses are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal–oral route, passed by hand-to-mouth contact or in food or water. Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection.
Plant form and function
The plant body is made up of organs that can be organized into two major organ systems: a root system and a shoot system.  The root system anchors the plants into place. The roots themselves absorb water and minerals and store photosynthetic products. The shoot system is composed of stem, leaves, and flowers. The stems hold and orient the leaves to the sun, which allow the leaves to conduct photosynthesis. The flowers are shoots that have been modified for reproduction. Shoots are composed of phytomers, which are functional units that consist of a node carrying one or more leaves, internode, and one or more buds.
A plant body has two basic patterns (apical–basal and radial axes) that been established during embryogenesis.  Cells and tissues are arranged along the apical-basal axis from root to shoot whereas the three tissue systems (dermal, ground, and vascular) that make up a plant's body are arranged concentrically around its radial axis.  The dermal tissue system forms the epidermis (or outer covering) of a plant, which is usually a single cell layer that consists of cells that have differentiated into three specialized structures: stomata for gas exchange in leaves, trichomes (or leaf hair) for protection against insects and solar radiation, and root hairs for increased surface areas and absorption of water and nutrients. The ground tissue makes up virtually all the tissue that lies between the dermal and vascular tissues in the shoots and roots. It consists of three cell types: Parenchyma, collenchyma, and sclerenchyma cells. Finally, the vascular tissues are made up of two constituent tissues: xylem and phloem. The xylem is made up two of conducting cells called tracheids and vessel elements whereas the phloem is characterized by the presence of sieve tube elements and companion cells. 
Plant nutrition and transport
Like all other organisms, plants are primarily made up of water and other molecules containing elements that are essential to life.  The absence of specific nutrients (or essential elements), many of which have been identified in hydroponic experiments, can disrupt plant growth and reproduction. The majority of plants are able to obtain these nutrients from solutions that surrounds their roots in the soil.  Continuous leaching and harvesting of crops can deplete the soil of its nutrients, which can be restored with the use of fertilizers. Carnivorous plants such as Venus flytraps are able to obtain nutrients by digesting other arthropods whereas parasitic plants such as mistletoes can parasitize other plants for water and nutrients.
Plants need water to conduct photosynthesis, transport solutes between organs, cool their leaves by evaporation, and maintain internal pressures that support their bodies.  Water is able to diffuse in and out of plant cells by osmosis. The direction of water movement across a semipermeable membrane is determined by the water potential across that membrane.  Water is able to diffuse across a root cell's membrane through aquaporins whereas solutes are transported across by the membrane by ion channels and pumps. In vascular plants, water and solutes are able to enter the xylem, a vascular tissue, by way of an apoplast and symplast. Once in the xylem, the water and minerals are distributed upward by transpiration from the soil to the aerial parts of the plant.   In contrast, the phloem, another vascular tissue, distributes carbohydrates (e.g., sucrose) and other solutes such as hormones by translocation from a source (e.g., mature leaf or root) in which they were produced to a sink (e.g., root, flower, or developing fruit) in which they will be used and stored.  Sources and sinks can switch roles, depending on the amount of carbohydrates accumulated or mobilized for the nourishment of other organs.
Plant development is regulated by environmental cues and the plant's own receptors, hormones, and genome.  Morever, they have several characteristics that allow them to obtain resources for growth and reproduction such as meristems, post-embryonic organ formation, and differential growth.
Development begins with a seed, which is an embryonic plant enclosed in a protective outer covering. Most plant seeds are usually dormant, a condition in which the seed's normal activity is suspended.  Seed dormancy may last may last weeks, months, years, and even centuries. Dormancy is broken once conditions are favorable for growth, and the seed will begin to sprout, a process called germination. Imbibition is the first step in germination, whereby water is absorbed by the seed. Once water is absorbed, the seed undergoes metabolic changes whereby enzymes are activated and RNA and proteins are synthesized. Once the seed germinates, it obtains carbohydrates, amino acids, and small lipids that serve as building blocks for its development. These monomers are obtained from the hydrolysis of starch, proteins, and lipids that are stored in either the cotyledons or endosperm. Germination is completed once embryonic roots called radicle have emerged from the seed coat. At this point, the developing plant is called a seedling and its growth is regulated by its own photoreceptor proteins and hormones. 
Unlike animals in which growth is determinate, i.e., ceases when the adult state is reached, plant growth is indeterminate as it is an open-ended process that could potentially be lifelong.  Plants grow in two ways: primary and secondary. In primary growth, the shoots and roots are formed and lengthened. The apical meristem produces the primary plant body, which can be found in all seed plants. During secondary growth, the thickness of the plant increases as the lateral meristem produces the secondary plant body, which can be found in woody eudicots such as trees and shrubs. Monocots do not go through secondary growth.  The plant body is generated by a hierarchy of meristems. The apical meristems in the root and shoot systems give rise to primary meristems (protoderm, ground meristem, and procambium), which in turn, give rise to the three tissue systems (dermal, ground, and vascular).
Most angiosperms (or flowering plants) engage in sexual reproduction.  Their flowers are organs that facilitate reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may facilitate two types of pollination: self-pollination and cross-pollination. Self-pollination occurs when the pollen from the anther is deposited on the stigma of the same flower, or another flower on the same plant. Cross-pollination is the transfer of pollen from the anther of one flower to the stigma of another flower on a different individual of the same species. Self-pollination happened in flowers where the stamen and carpel mature at the same time, and are positioned so that the pollen can land on the flower’s stigma. This pollination does not require an investment from the plant to provide nectar and pollen as food for pollinators. 
Like animals, plants produce hormones in one part of its body to signal cells in another part to respond. The ripening of fruit and loss of leaves in the winter are controlled in part by the production of the gas ethylene by the plant. Stress from water loss, changes in air chemistry, or crowding by other plants can lead to changes in the way a plant functions. These changes may be affected by genetic, chemical, and physical factors.
To function and survive, plants produce a wide array of chemical compounds not found in other organisms. Because they cannot move, plants must also defend themselves chemically from herbivores, pathogens and competition from other plants. They do this by producing toxins and foul-tasting or smelling chemicals. Other compounds defend plants against disease, permit survival during drought, and prepare plants for dormancy, while other compounds are used to attract pollinators or herbivores to spread ripe seeds.
Many plant organs contain different types of photoreceptor proteins, each of which reacts very specifically to certain wavelengths of light.  The photoreceptor proteins relay information such as whether it is day or night, duration of the day, intensity of light available, and the source of light. Shoots generally grow towards light, while roots grow away from it, responses known as phototropism and skototropism, respectively. They are brought about by light-sensitive pigments like phototropins and phytochromes and the plant hormone auxin.  Many flowering plants bloom at the appropriate time because of light-sensitive compounds that respond to the length of the night, a phenomenon known as photoperiodism.
In addition to light, plants can respond to other types of stimuli. For instance, plants can sense the direction of gravity to orient themselves correctly. They can respond to mechanical stimulation. 
Animal form and function
The cells in each animal body are bathed in interstitial fluid, which make up the cell's environment. This fluid and all its characteristics (e.g., temperature, ionic composition) can be described as the animal's internal environment, which is in contrast to the external environment that encompasses the animal's outside world.  Animals can be classified as either regulators or conformers. Animals such as mammals and birds are regulators as they are able to maintain a constant internal environment such as body temperature despite their environments changing. These animals are also described as homeotherms as they exhibit thermoregulation by keeping their internal body temperature constant. In contrast, animals such as fishes and frogs are conformers as they adapt their internal environment (e.g., body temperature) to match their external environments. These animals are also described as poikilotherms or ectotherms as they allow their body temperatures to match their external environments. In terms of energy, regulation is more costly than conformity as an animal expands more energy to maintain a constant internal environment such as increasing its basal metabolic rate, which is the rate of energy consumption.  Similarly, homeothermy is more costly than poikilothermy. Homeostasis is the stability of an animal's internal environment, which is maintained by negative feedback loops.  
The body size of terrestrial animals vary across different species but their use of energy does not scale linearly according to their size.  Mice, for example, are able to consume three times more food than rabbits in proportion to their weights as the basal metabolic rate per unit weight in mice is greater than in rabbits.  Physical activity can also increase an animal's metabolic rate. When an animal runs, its metabolic rate increases linearly with speed.  However, the relationship is non-linear in animals that swim or fly. When a fish swims faster, it encounters greater water resistance and so its metabolic rates increases exponential.  Alternatively, the relationship of flight speeds and metabolic rates is U-shaped in birds.  At low flight speeds, a bird must maintain a high metabolic rates to remain airborne. As it speeds up its flight, its metabolic rate decreases with the aid of air rapidly flows over its wings. However, as it increases in its speed even further, its high metabolic rates rises again due to the increased effort associated with rapid flight speeds. Basal metabolic rates can be measured based on an animal's rate of heat production.
Water and salt balance
An animal's body fluids have three properties: osmotic pressure, ionic composition, and volume.  Osmotic pressures determine the direction of the diffusion of water (or osmosis), which moves from a region where osmotic pressure (total solute concentration) is low to a region where osmotic pressure (total solute concentration) is high. Aquatic animals are diverse with respect to their body fluid compositions and their environments. For example, most invertebrate animals in the ocean have body fluids that are isosmotic with seawater. In contrast, ocean bony fishes have body fluids that are hyposmotic to seawater. Finally, freshwater animals have body fluids that are hyperosmotic to fresh water. Typical ions that can be found in an animal's body fluids are sodium, potassium, calcium, and chloride. The volume of body fluids can be regulated by excretion. Vertebrate animals have kidneys, which are excretory organs made up of tiny tubular structures called nephrons, which make urine from blood plasma. The kidneys' primary function is to regulate the composition and volume of blood plasma by selectively removing material from the blood plasma itself. The ability of xeric animals such as kangaroo rats to minimize water loss by producing urine that is 10-20 times concentrated than their blood plasma allows them to adapt in desert environments that receive very little precipitation. 
Nutrition and digestion
Animals are heterotrophs as they feed on other living organisms to obtain energy and organic compounds.  They are able to obtain food in three major ways such as targeting visible food objects, collecting tiny food particles, or depending on microbes for critical food needs. The amount of energy stored in food can be quantified based on the amount of heat (measured in calories or kilojoules) emitted when the food is burnt in the presence of oxygen. If an animal were to consume food that contains an excess amount of chemical energy, it will store most of that energy in the form of lipids for future use and some of that energy as glycogen for more immediate use (e.g., meeting the brain's energy needs).  The molecules in food are chemical building blocks that are needed for growth and development. These molecules include nutrients such as carbohydrates, fats, and proteins. Vitamins and minerals (e.g., calcium, magnesium, sodium, and phosphorus) are also essential. The digestive system, which typically consist of a tubular tract that extends from the mouth to the anus, is involved in the breakdown (or digestion) of food into small molecules as it travels down peristaltically through the gut lumen shortly after it has been ingested. These small food molecules are then absorbed into the blood from the lumen, where they are then distributed to the rest of the body as building blocks (e.g., amino acids) or sources of energy (e.g., glucose). 
In addition to their digestive tracts, vertebrate animals have accessory glands such as a liver and pancreas as part of their digestive systems.  The processing of food in these animals begins in the foregut, which includes the mouth, esophagus, and stomach. Mechanical digestion of food starts in the mouth with the esophagus serving as a passageway for food to reach the stomach, where it is stored and disintegrated (by the stomach's acid) for further processing. Upon leaving the stomach, food enters into the midgut, which is the first part of the intestine (or small intestine in mammals) and is the principal site of digestion and absorption. Food that does not get absorbed are stored as indigestible waste (or feces) in the hindgut, which is the second part of the intestine (or large intestine in mammals). The hindgut then completes the reabsorption of needed water and salt prior to eliminating the feces from the rectum. 
The respiratory system consists of specific organs and structures used for gas exchange in animals and plants. The anatomy and physiology that make this happen varies greatly, depending on the size of the organism, the environment in which it lives and its evolutionary history. In land animals the respiratory surface is internalized as linings of the lungs.  Gas exchange in the lungs occurs in millions of small air sacs in mammals and reptiles these are called alveoli, and in birds they are known as atria. These microscopic air sacs have a very rich blood supply, thus bringing the air into close contact with the blood.  These air sacs communicate with the external environment via a system of airways, or hollow tubes, of which the largest is the trachea, which branches in the middle of the chest into the two main bronchi. These enter the lungs where they branch into progressively narrower secondary and tertiary bronchi that branch into numerous smaller tubes, the bronchioles. In birds the bronchioles are termed parabronchi. It is the bronchioles, or parabronchi that generally open into the microscopic alveoli in mammals and atria in birds. Air has to be pumped from the environment into the alveoli or atria by the process of breathing which involves the muscles of respiration.
A circulatory system usually consists of a muscular pump such as a heart, a fluid (blood), and system of blood vessels that deliver it.   Its principal function is to transport blood and other substances to and from cell (biology)s and tissues. There are two types of circulatory systems: open and closed. In open circulatory systems, blood exits blood vessels as it circulates throughout the body whereas in closed circulatory system, blood is contained within the blood vessels as it circulates. Open circulatory systems can be observed in invertebrate animals such as arthropods (e.g., insects, spiders, and lobsters) whereas closed circulatory systems can be found in vertebrate animals such as fishes, amphibians, and mammals. Circulation in animals occur between two types of tissues: systemic tissues and breathing (or pulmonary) organs.  Systemic tissues are all the tissues and organs that make up an animal's body other than its breathing organs. Systemic tissues take up oxygen but adds carbon dioxide to the blood whereas a breathing organs takes up carbon dioxide but add oxygen to the blood.  In birds and mammals, the systemic and pulmonary systems are connected in series.
In the circulatory system, blood is important because it is the means by which oxygen, carbon dioxide, nutrients, hormones, agents of immune system, heat, wastes, and other commodities are transported.  In annelids such as earthworms and leeches, blood is propelled by peristaltic waves of contractions of the heart muscles that make up the blood vessels. Other animals such as crustaceans (e.g., crayfish and lobsters), have more than one heart to propel blood throughout their bodies. Vertebrate hearts are multichambered and are able to pump blood when their ventricles contract at each cardiac cycle, which propels blood through the blood vessels.  Although vertebrate hearts are myogenic, their rate of contraction (or heart rate) can be modulated by neural input from the body's autonomic nervous system.
Muscle and movement
In vertebrates, the muscular system consists of skeletal, smooth and cardiac muscles. It permits movement of the body, maintains posture and circulates blood throughout the body.  Together with the skeletal system, it forms the musculoskeletal system, which is responsible for the movement of vertebrate animals.  Skeletal muscle contractions are neurogenic as they require synaptic input from motor neurons. A single motor neuron is able to innervate multiple muscle fibers, thereby causing the fibers to contract at the same time. Once innervated, the protein filaments within each skeletal muscle fiber slide past each other to produce a contraction, which is explained by the sliding filament theory. The contraction produced can be described as a twitch, summation, or tetanus, depending on the frequency of action potentials. Unlike skeletal muscles, contractions of smooth and cardiac muscles are myogenic as they are initiated by the smooth or heart muscle cells themselves instead of a motor neuron. Nevertheless, the strength of their contractions can be modulated by input from the autonomic nervous system. The mechanisms of contraction are similar in all three muscle tissues.
In invertebrates such as earthworms and leeches, circular and longitudinal muscles cells form the body wall of these animals and are responsible for their movement.  In an earthworm that is moving through a soil, for example, contractions of circular and longitudinal muscles occur reciprocally while the coelomic fluid serves as a hydroskeleton by maintaining turgidity of the earthworm.  Other animals such as mollusks, and nematodes, possess obliquely striated muscles, which contain bands of thick and thin filaments that are arranged helically rather than transversely, like in vertebrate skeletal or cardiac muscles.  Advanced insects such as wasps, flies, bees, and beetles possess asynchronous muscles that constitute the flight muscles in these animals.  These flight muscles are often called fibrillar muscles because they contain myofibrils that are thick and conspicuous. 
The nervous system is a network of cells that processes sensory information and generates behaviors. At the cellular level, the nervous system is defined by the presence of neurons, which are cells specialized to handle information.  They can transmit or receive information at sites of contacts called synapses.  More specifically, neurons can conduct nerve impulses (or action potentials) that travel along their thin fibers called axons, which can then be transmitted directly to a neighboring cell through electrical synapses or cause chemicals called neurotransmitters to be released at chemical synapses. According to the sodium theory, these action potentials can be generated by the increased permeability of the neuron's cell membrane to sodium ions.  Cells such as neurons or muscle cells may be excited or inhibited upon receiving a signal from another neuron. The connections between neurons can form neural pathways, neural circuits, and larger networks that generate an organism's perception of the world and determine its behavior. Along with neurons, the nervous system contains other specialized cells called glia or glial cells, which provide structural and metabolic support.
Nervous systems are found in most multicellular animals, but vary greatly in complexity.  In vertebrates, the nervous system consists of the central nervous system (CNS), which includes the brain and spinal cord, and the peripheral nervous system (PNS), which consists of nerves that connect the CNS to every other part of the body. Nerves that transmit signals from the CNS are called motor nerves or efferent nerves, while those nerves that transmit information from the body to the CNS are called sensory nerves or afferent nerves. Spinal nerves are mixed nerves that serve both functions. The PNS is divided into three separate subsystems, the somatic, autonomic, and enteric nervous systems. Somatic nerves mediate voluntary movement. The autonomic nervous system is further subdivided into the sympathetic and the parasympathetic nervous systems. The sympathetic nervous system is activated in cases of emergencies to mobilize energy, while the parasympathetic nervous system is activated when organisms are in a relaxed state. The enteric nervous system functions to control the gastrointestinal system. Both autonomic and enteric nervous systems function involuntarily. Nerves that exit directly from the brain are called cranial nerves while those exiting from the spinal cord are called spinal nerves.
Many animals have sense organs that can detect their environment. These sense organs contain sensory receptors, which are sensory neurons that convert stimuli into electrical signals.  Mechanoreceptors, for example, which can be found in skin, muscle, and hearing organs, generate action potentials in response to changes in pressures.   Photoreceptor cells such as rods and cones, which are part of the vertebrate retina, can respond to specific wavelengths of light.   Chemoreceptors detect chemicals in the mouth (taste) or in the air (smell). 
Hormones are signaling molecules transported in the blood to distant organs to regulate their function.   Hormones are secreted by internal glands that are part of an animal's endocrine system. In vertebrates, the hypothalamus is the neural control center for all endocrine systems. In humans specifically, the major endocrine glands are the thyroid gland and the adrenal glands. Many other organs that are part of other body systems have secondary endocrine functions, including bone, kidneys, liver, heart and gonads. For example, kidneys secrete the endocrine hormone erythropoietin. Hormones can be amino acid complexes, steroids, eicosanoids, leukotrienes, or prostaglandins.  The endocrine system can be contrasted to both exocrine glands, which secrete hormones to the outside of the body, and paracrine signaling between cells over a relatively short distance. Endocrine glands have no ducts, are vascular, and commonly have intracellular vacuoles or granules that store their hormones. In contrast, exocrine glands, such as salivary glands, sweat glands, and glands within the gastrointestinal tract, tend to be much less vascular and have ducts or a hollow lumen.
Animals can reproduce in one of two ways: asexual and sexual. Nearly all animals engage in some form of sexual reproduction.  They produce haploid gametes by meiosis. The smaller, motile gametes are spermatozoa and the larger, non-motile gametes are ova.  These fuse to form zygotes,  which develop via mitosis into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed, and develop into a new sponge.  In most other groups, the blastula undergoes more complicated rearrangement.  It first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm.  In most cases, a third germ layer, the mesoderm, also develops between them.  These germ layers then differentiate to form tissues and organs.  Some animals are capable of asexual reproduction, which often results in a genetic clone of the parent. This may take place through fragmentation budding, such as in Hydra and other cnidarians or parthenogenesis, where fertile eggs are produced without mating, such as in aphids.  
Animal development begins with the formation of a zygote that results from the fusion of a sperm and egg during fertilization.  The zygote undergoes a rapid multiple rounds of mitotic cell period of cell divisions called cleavage, which forms a ball of similar cells called a blastula. Gastrulation occurs, whereby morphogenetic movements convert the cell mass into a three germ layers that comprise the ectoderm, mesoderm and endoderm.
The end of gastrulation signals the beginning of organogenesis, whereby the three germ layers form the internal organs of the organism.  The cells of each of the three germ layers undergo differentiation, a process where less-specialized cells become more-specialized through the expression of a specific set of genes. Cellular differentiation is influenced by extracellular signals such as growth factors that are exchanged to adjacent cells, which is called juxtracrine signaling, or to neighboring cells over short distances, which is called paracrine signaling.   Intracellular signals consist of a cell signaling itself (autocrine signaling), also play a role in organ formation. These signaling pathways allows for cell rearrangement and ensures that organs form at specific sites within the organism.  
The immune system is a network of biological processes that detects and responds to a wide variety of pathogens. Many species have two major subsystems of the immune system. The innate immune system provides a preconfigured response to broad groups of situations and stimuli. The adaptive immune system provides a tailored response to each stimulus by learning to recognize molecules it has previously encountered. Both use molecules and cells to perform their functions.
Nearly all organisms have some kind of immune system. Bacteria have a rudimentary immune system in the form of enzymes that protect against virus infections. Other basic immune mechanisms evolved in ancient plants and animals and remain in their modern descendants. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system. Jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt to recognize pathogens more efficiently. Adaptive (or acquired) immunity creates an immunological memory leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.
Behaviors play a central a role in animals' interaction with each other and with their environment.  They are able to use their muscles to approach one another, vocalize, seek shelter, and migrate. An animal's nervous system activates and coordinates its behaviors. Fixed action patterns, for instance, are genetically determined and stereotyped behaviors that occur without learning.   These behaviors are under the control of the nervous system and can be quite elaborate.  Examples include the pecking of kelp gull chicks at the red dot on their mother's beak. Other behaviors that have emerged as a result of natural selection include foraging, mating, and altruism.  In addition to evolved behavior, animals have evolved the ability to learn by modifying their behaviors as a result of early individual experiences. 
Ecology is the study of the distribution and abundance of living organisms, the interaction between them and their environment.  The community of living (biotic) organisms in conjunction with the nonliving (abiotic) components (e.g., water, light, radiation, temperature, humidity, atmosphere, acidity, and soil) of their environment is called an ecosystem.    These biotic and abiotic components are linked together through nutrient cycles and energy flows.  Energy from the sun enters the system through photosynthesis and is incorporated into plant tissue. By feeding on plants and on one another, animals play an important role in the movement of matter and energy through the system. They also influence the quantity of plant and microbial biomass present. By breaking down dead organic matter, decomposers release carbon back to the atmosphere and facilitate nutrient cycling by converting nutrients stored in dead biomass back to a form that can be readily used by plants and other microbes. 
The Earth's physical environment is shaped by solar energy and topography.  The amount of solar energy input varies in space and time due to the spherical shape of the Earth and its axial tilt. Variation in solar energy input drives weather and climate patterns. Weather is the day-to-day temperature and precipitation activity, whereas climate is the long-term average of weather, typically averaged over a period of 30 years.   Variation in topography also produces environmental heterogeneity. On the windward side of a mountain, for example, air rises and cools, with water changing from gaseous to liquid or solid form, resulting in precipitation such as rain or snow.  As a result, wet environments allow for lush vegetation to grow. In contrast, conditions tend to be dry on the leeward side of a mountain due to the lack of precipitation as air descends and warms, and moisture remains as water vapor in the atmosphere. Temperature and precipitation are the main factors that shape terrestrial biomes.
A population is the number of organisms of the same species that occupy an area and reproduce from generation to generation.      Its abundance can be measured using population density, which is the number of individuals per unit area (e.g., land or tree) or volume (e.g., sea or air).  Given that it is usually impractical to count every individual within a large population to determine its size, population size can be estimated by multiplying population density by the area or volume. Population growth during short-term intervals can be determined using the population growth rate equation, which takes into consideration birth, death, and immigration rates. In the longer term, the exponential growth of a population tends to slow down as it reaches its carrying capacity, which can be modeled using the logistic equation.  The carrying capacity of an environment is the maximum population size of a species that can be sustained by that specific environment, given the food, habitat, water, and other resources that are available.  The carrying capacity of a population can be affected by changing environmental conditions such as changes in the availability resources and the cost of maintaining them. In human populations, new technologies such as the Green revolution have helped increase the Earth's carrying capacity for humans over time, which has stymied the attempted predictions of impending population decline, the famous of which was by Thomas Malthus in the 18th century. 
A community is a group of populations of two or more different species occupying the same geographical area at the same time. A biological interaction is the effect that a pair of organisms living together in a community have on each other. They can be either of the same species (intraspecific interactions), or of different species (interspecific interactions). These effects may be short-term, like pollination and predation, or long-term both often strongly influence the evolution of the species involved. A long-term interaction is called a symbiosis. Symbioses range from mutualism, beneficial to both partners, to competition, harmful to both partners. 
Every species participates as a consumer, resource, or both in consumer–resource interactions, which form the core of food chains or food webs.  There are different trophic levels within any food web, with the lowest level being the primary producers (or autotrophs) such as plants and algae that convert energy and inorganic material into organic compounds, which can then be used by the rest of the community.    At the next level are the heterotrophs, which are the species that obtain energy by breaking apart organic compounds from other organisms.  Heterotrophs that consume plants are primary consumers (or herbivores) whereas heterotrophs that consume herbivores are secondary consumers (or carnivores). And those that eat secondary consumers are tertiary consumers and so on. Omnivorous heterotrophs are able to consume at multiple levels. Finally, there are decomposers that feed on the waste products or dead bodies of organisms. 
On average, the total amount of energy incorporated into the biomass of a trophic level per unit of time is about one-tenth of the energy of the trophic level that it consumes. Waste and dead material used by decomposers as well as heat lost from metabolism make up the other ninety percent of energy that is not consumed by the next trophic level. 
In the global ecosystem (or biosphere), matter exist as different interacting compartments, which can be biotic or abiotic as well as accessible or inaccessible, depending on their forms and locations.  For example, matter from terrestrial autotrophs are both biotic and accessible to other living organisms whereas the matter in rocks and minerals are abiotic and inaccessible to living organisms. A biogeochemical cycle is a pathway by which specific elements of matter are turned over or moved through the biotic (biosphere) and the abiotic (lithosphere, atmosphere, and hydrosphere) compartments of Earth. There are biogeochemical cycles for nitrogen, carbon, and water. In some cycles there are reservoirs where a substance remains or is sequestered for a long period of time.
Climate change includes both global warming driven by human-induced emissions of greenhouse gases and the resulting large-scale shifts in weather patterns. Though there have been previous periods of climatic change, since the mid-20th century humans have had an unprecedented impact on Earth's climate system and caused change on a global scale.  The largest driver of warming is the emission of greenhouse gases, of which more than 90% are carbon dioxide and methane.  Fossil fuel burning (coal, oil, and natural gas) for energy consumption is the main source of these emissions, with additional contributions from agriculture, deforestation, and manufacturing.  Temperature rise is accelerated or tempered by climate feedbacks, such as loss of sunlight-reflecting snow and ice cover, increased water vapor (a greenhouse gas itself), and changes to land and ocean carbon sinks.
Conservation biology is the study of the conservation of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions.    It is concerned with factors that influence the maintenance, loss, and restoration of biodiversity and the science of sustaining evolutionary processes that engender genetic, population, species, and ecosystem diversity.     The concern stems from estimates suggesting that up to 50% of all species on the planet will disappear within the next 50 years,  which has contributed to poverty, starvation, and will reset the course of evolution on this planet.   Biodiversity affects the functioning of ecosystems, which provide a variety of services upon which people depend.
Conservation biologists research and educate on the trends of biodiversity loss, species extinctions, and the negative effect these are having on our capabilities to sustain the well-being of human society. Organizations and citizens are responding to the current biodiversity crisis through conservation action plans that direct research, monitoring, and education programs that engage concerns at local through global scales.    
What is Evolutionary Biology/meaning/concept
There are more than two million species of living things. This great diversity of organisms seems to have been designed to guarantee their existence. In this sense, the theory that explains how each organism adapts to its environment is known as the theory of evolution , which is the scientific benchmark of evolutionary biology.
Every living thing has specifically adapted over millions of years of evolution. This raises one of the great challenges of evolutionary biology. The problem can be stated as a question: if each species is adapted to its environment, it is worth asking how can it survive the changes that occur over time?
According to biologists, life in any of its forms has a basic quality: reproduction.
In any environment, individuals of each species reproduce and each individual must compete with their own species to survive. Thus, according to the principles of evolutionary biology, only living beings that best adapt to their environment survive. This is because each individual is different from the other and only those whose characteristics are useful can survive.
The theory of evolution established a scientific revolution
This conception of life is based on the researches of the British scientist Charles Darwin (1809-1882). According to Darwin, the process that explains the changes of each species is known as natural selection. Evolutionary Biology
Darwin’s theory of evolution was exposed in his work “The Origin of Species”, a work that revolutionized biology, other branches of knowledge and the view of the world in general. Darwin explained the complexity and diversity of life as a whole.
The fundamentals of natural selection
Before Darwin’s explanations, species were believed to be created by the hand of God. But their research brought a very different conception.
Darwin’s natural selection is based on two aspects:
1) the reproductive capacity of the animal population is practically unlimited, but resources are scarce and this incompatibility imposes a struggle for survival among individuals of each species Evolutionary Biology
2) in the struggle for survival, there is a selection of physical traits (phenotypes) that are more favorable.
These two mechanisms contribute to the diversification of species and their adaptation to the natural environment. Evolutionary Biology
Reviewed by Jan Just, Instructor of Biology, Portland Community College on 6/13/21
Principles of Biology: Biology 211, 212, 213 is missing the diversity of life unit, the plant anatomy and physiology unit, and the animal anatomy and physiology unit. The missing units constitute approximately 1/3 of the material covered in most. read more
Reviewed by Jan Just, Instructor of Biology, Portland Community College on 6/13/21
Comprehensiveness rating: 3 see less
Principles of Biology: Biology 211, 212, 213 is missing the diversity of life unit, the plant anatomy and physiology unit, and the animal anatomy and physiology unit. The missing units constitute approximately 1/3 of the material covered in most publisher-based majors biology textbooks.
Content Accuracy rating: 4
Topics in this book are not discussed at the level of detail consistent with other publisher-based majors biology textbooks.
Relevance/Longevity rating: 5
I like that this textbook contains current information on topics such as biodiversity and climate change. These aspects will need to be frequently updated and I believe that the format of this book will make that relatively easy.
This textbook often uses a tone that sounded conversational to me. I would be interested to hear a student's point of view about whether this makes the textbook more accessible and less intimidating.
This book is organized in a consistent pattern throughout.
Each topic is broken down into logical subtopics and the format of these subtopics is consistent throughout the book. Whole sections, or subunits could be utilized independently.
Organization/Structure/Flow rating: 5
The overall topics for this book are consistent with the order in which they are typically presented in majors biology textbooks. Within each section there is a general description followed by a logical progression of subunits.
Some charts and graphs were too small to read and understand easily. In one instance there is a n image related to phenylketonuria that appears between two unrelated paragraphs and the image is repeated in the appropriate place.
Grammatical Errors rating: 4
As a whole the text is grammatically correct
Cultural Relevance rating: 3
Humans are not the primary source of examples throughout this textbook, which is appropriate and consistent with other similar books. With topics such as inheritance and population growth there are opportunities for inclusive examples or for clarifying details that would more fully encompass a variety of races, ethnicities, and backgrounds.
It is important to understand that the flagship publisher textbook for majors biology took 9 years to develop its first edition in 1987 and has had many revisions and additions since. Writing an OER text for a major biology course is a monumental undertaking and I believe that this text will continue to improve over time as additional topics and increased detail are added. This textbook could be used for gaining fundamental concepts in conjunction with a course that employs open pedagogy and uses a variety of additional resources and materials.
Reviewer 1: Valerian Dolja, Oregon State University
This is another installation in the series of Koonin solo and Koonin & Wolf duo papers dealing with the most fundamental and hotly debated problems of evolutionary genomics. It is very timely, incisive, cool, pragmatic, certainly, not "the final truth", but about the best that can be offered at the moment. It also helps that the style of the paper shows enviable intellectual candor and clarity. Although I am not directly involved in the TOL business, I felt compelled to review this paper even from a prospective of a virologist interested in the big picture of life origin and evolution.
One conclusion of the essay, that the pursuit of a 'simple and true' organismal TOL is over due to overwhelming contributions of HGT to the life histories of viruses, prokaryotes, and unicellular eukaryotes, the organisms that together represent the substantial majority of genetic universe, is the only conclusion fully compatible with the results of comparative genomics. Another major conclusion, that evolution of individual genes is faithfully represented by trees, whereas evolution of organisms (or, preferably, genomes) can only be rendered as a FOL, also seems to be an inevitable outcome of the presented logical analysis of the units and processes of molecular evolution. Importantly, these conclusions provide a sensible and constructive alternative to the fierce and increasingly futile argument about the viability of the TOL.
Having said this, I would like to comment on two particular aspects of the analysis offered by Koonin and Wolf.
1. After going through two incarnations of the work, I am not yet at peace with the FUE definition. I would prefer defining FUE as a genomic unit encoding protein, protein domain, structural or regulatory RNA, or a control element with independent evolutionary history. [Evolutionary Unit of a Genome, or EUG]. I do not see a need in categorizing FUEs into selfish elements such as viruses on one hand, and regular genes on the other. First, selfish elements, with the exception of viroids, are ensembles of 'regular genes' even though some of them encode replication-related functions. Second, some of the regular genes of the 'non-selfish', that is, cellular genomes, are also involved in replication. Third, both selfish elements and cellular genomes are collections of genes of various 'selfishness quotient', all of which are equal subjects to HGT. Therefore, both cellular and noncellular genomes represent the same genetic continuum that can be analyzed in its entirety using the same rules and approaches.
Authors' response: We do not really see any contradiction between the FUE definition and the EUG definition suggested by Dolja (we do appreciate the EUphony of the latter). As for partitioning of the FUEs into the selfish and non-selfish classes, we tend to believe that the validity and usefulness of this classification is an open question that is subject to quantitative analysis using an appropriate mathematical framework and the available extensive comparative-genomic data. Indeed, any FUE, in principle, can be assigned a 'selfishness quotient'. However, the correct formula for this quotient let alone the distribution of its values across FUEs remain unknowns. Once this formula is derived and the distribution is drawn, the issue of the classification of FUEs will become tractable. If the distribution turns out to be bimodal, the two classes will be rectified if by contrast, the distribution is unimodal, the continuum model will be more appropriate. This problem is the target of an ongoing investigation in our group.
2. I am not sure I can fully agree with the statement that the FUE rather than the organism or species (or, better, the genome) is the only fundamental agency of evolution. The genome is, indeed, a true unit of replication, and as such, also has a unique evolutionary history. Focusing solely on FUEs leaves behind the entire realm of population genetics that, as groundbreaking work of Michael Lynch has demonstrated, is one of the major determinants of the evolution of genome architecture. In other words, the laws of genome evolution are not reducible merely to sum total of FUEs' evolutionary histories because how the ensemble of FUEs put together depends in large part on population dynamics that is not determined by FUEs per se.
Authors' response: We do not agree with such a categorical statement either and do not believe that it is contained or even implied in this article. Genomes are also fundamental and so are populations of organisms. However, in some ways, in particular, with respect to evolutionary independence and the applicability of trees as models of evolution FUEs appear. well, more equal than those other units. As for the groundbreaking work of Lynch, this is a bit ironic but a good idea to clarify. Lynch actually emphasizes that the effective population size, even in eukaryotes, where horizontal transfer is not much of an issue, the effective population size (the key parameter of the theory) is, generally, different for different genes. So we are not at all leaving behind population genetics which is indeed crucial for understanding evolution at any level - it seems that the true unit of evolution within the population-genetic framework is. a FUE.
Reviewer 2: W. Ford Doolittle, Dalhousie University
Koonin and Wolf aptly present one of the several possible responses to the Tree of Life kerfuffle, although their paper won't likely make the conflict just go away, as they and many readers no doubt wish. What these authors hope to do is displace the Tree of Life with a "Forest of Life" as the all-embracing metaphor for the history of living things. This is progress within the paradigm, to be sure, and I think they are right to point out, for instance, that because homologous recombination falls off as gene sequences diverge but lateral gene transfer uses mechanisms that are indifferent to gene sequence, gene evolution is inherently tree-like while genome evolution is not.
What I am less sure of is that we really need to "define the primary units and the fundamental patterns and processes of evolution". It is this kind of deep metatheoretical approach that gave us the Tree of Life in the first place and that keeps us on the hotseat in the ongoing struggle against the proponents of intelligent design and other nonsensical nonscience. Really, we understand pretty well all the individual genetic, population, ecological and environmental mechanisms that effect the evolution of genes, genomes, organisms and species, and we waste our times (and make ourselves vulnerable to creationist pettifoggery) by imagining there are causal processes or patterns deeper than these that we need to conceptualize. (The introduction of graph theoretical language really does not get us any closer to some fundamental truth, I think.)
It may well be sensible to talk about Fundamental Unit (s) of Evolution (FUE), but authors have a rather limited range of such units they will consider, and perhaps too much faith in their boundedness. Organisms, populations and even species can be FUEs, and over their own appropriate time scales are every bit as much "fundamental units of life" as are genes, while all sorts of entities in between can "evolve coherently for a certain time span." Again, I question the sense of describing one level or unit as more fundamental than another, but such is common practice and no reason not to consider this a valuable contribution in that tradition. So the rest of my remarks will be quibbles about specifics.
Authors' response: We realize the dangers (and the seductions) of metanarratives . And yet, we also tend to think that, in different domains of physical reality, there are distinct levels that are central to the adequate description and "understanding" of each domain. Molecules are fundamental to (bio)chemistry, cells to physiology (broadly construed), stars to astrophysics, galaxies to cosmology. In the same sense, we maintain that our FUEs are fundamental units of evolution which by no means applies that other levels are unimportant.
In my copy of the Origin, its only figure appears eight pages before the quoted passage, and is clearly meant to illustrate evolution of the "species of a genus large in its own country", not the great tree 'simile" whose veracity Darwin accepted. The quote does not "introduce" the figure. Not that this should really matter: it's remarkable the extent to which accurate readings of Darwin seem essential to the credibility of current theory, as if evolutionary biology actually were the quasi-religious enterprise our opponents treat it as.
Authors' response: although there is absolutely no religious bend in our attitude to Darwin (or anyone/thing else), we do maintain that the Origin is, possibly, THE greatest book ever published, so precision is highly desirable when it is discussed, and correction much appreciated. The respective text was modified to eliminate any misrepresentation.
The Spiegelman experiments were certainly exciting and important (and I had the good fortune to have summer jobs in Sol's lab while they were going on). But I think that what impressed the community about these experiments was that they actually worked, and so well, rather than that they proved that evolution could occur as "straightforward consequence of genetic material replication". Probably no one doubted that.
Authors' response: Seems to be a bit of a semantic issue. Perhaps, no one questioned evolution "in principle". but few believed it would work "so well". We emphasize this aspect in the revision: "including drastic changes to the evolving molecules".
I don't think we (ref. ) really meant that tree-thinking is not relevant in biology, but rather that it was only one way to think about biology.
Authors' response: we wrote "not a priori relevant" which makes a difference. In any case, in the revision, it is "so "tree thinking" was deemed not to be a priori relevant in biology or, in the very least, not necessarily central in biology".
The authors' view (which I share) that all or most all gene families have different evolutionary histories entails that the different last common ancestral versions of the different gene families existed at different times in the past, in different genomes. There was no LUCA, if by that we mean a single cell whose genome contained the ancestors of all modern genes. It really makes no sense to think of a population as "the ancestor", which is what I think authors mean by the statement "there is no reasonable doubt as to the reality of the collective stage". Today's cells comprise a population that derives from successively earlier populations, but there is no principled way to designate any one of these as LUCA.
Authors' response: Actually, we largely agree with this position on LUCA [45, 52] and argue elsewhere that it is probably more appropriate to speak of LUCAS, the Last Universal Common Ancestral State [55, 68]. Here, however, we were disinclined to take a strong stance on this issue that is not really the subject of the article.
Reviewer 3: Nicolas Galtier, CNRS - Université Montpellier 2
This paper exposes the pros and cons of using trees to represent evolution, especially in prokaryotes. Genes or gene portions are defined as fundamental evolving entities (FUEs), and the relationship between gene trees, species trees, and the "tree of life" are discussed. I liked the direct and provocative tone of the text, and the clarity of the viewpoint newly expressed.
- Statements with which I fully agree
1. Evolution results from replication with error.
2. Trees are a natural, useful representation of evolving molecules (genes).
3. The forest of gene trees is to be searched for patterns and trends.
4. The central trend has a strong, obvious meaning in animals and plants (if one appropriately accounts for endosymbiosis), less clearly so in microorganisms, depending on the prevalence of horizontal gene transfer.
- Statements which I think could deserve additional empirical support
5. Within-gene nonhomologous recombination (i.e., HGT of pieces of genes) is rare.
I am not sure this issue has been examined with the necessary care. People typically build gene trees, without systematically checking potential conflicts between portions of genes.
Authors' response: It is true that this has not been empirically studied with the necessary care and detail, and in the revised manuscript we changed the language to reflect this. We also cite a recent study that at least demonstrates preferential recombination outside regions encoding relatively small domains .
There are substantial levels of horizontal gene transfer in unicellular eukaryotes
I'm not sure which studies this statement refers to, and which taxa are concerned.
Authors' response: There is actually considerable amount of data on different unicellular eukaryotes. As it is not our intention here to get into the details on this particular subject, in the revised text, we cite two review articles that summarize the detected instances of HGT in unicellular eukaryotes [60, 61]
- Statements with which I am not sure I agree
7. Genes as the fundamental evolving unit
The definition of FUEs (Fundamental Units of Evolution) is the most original, and perhaps controversial, aspect of this manuscript. It is proposed that not only self-replicating genes, but also regular genes (or protein domains), should be considered the basic evolutionary entities, genomes (species) being seen as transient groups of genes of little evolutionary relevance. Although formally conceivable and intellectually appealing, I am not sure this view will prove to be a useful representation of the evolutionary process.
First, I note that FUEs are defined operationally: we essentially call FUE a maximal (in size) genetic element whose evolutionary history can be unambiguously represented by a single, bifurcating tree. Then, page 12, it is said that FUEs are "subject to selection independently of other FUEs". This is an important, questionable shift, which I think reveals a fundamental problem we have with HGT: the decoupling of transmission and selection (of the genetic material). Genomes (organisms), not genes, are the competing entities, between which natural selection operates, but genes can sometimes be transmitted between genomes.
Authors' response: There are several fundamental issues here, and there might be some genuine conceptual disagreement. We strongly believe that selection is a multilevel phenomenon that does affect individual FUEs although it certainly also acts at ensembles of FUEs, up to the organismal and, possibly, higher levels. Furthermore, it seems important to mephasize that we do not define a FUE as «genetic element whose evolutionary history can be unambiguously represented by a single, bifurcating tree». What we argue is that tree-like evolution is an inalienable property of FUEs. Furthermore, we also believe that there is a strong, intrinsic link between transmission and selection of genetic elements that works both ways: elements that are subject to selection are most likely to be transmitted, and elements that have a high transmission potential are the most selectable ones.
The logical but somewhat extreme viewpoint taken in this manuscript, in which transmission units are called evolutionary units (irrespective of selection units), appears to me not devoid of problems. For instance, it calls "evolving" items (genes) that most biologists would not call "living", although evolution is central in, e.g., Maynard-Smith's definition of life. The FUE concept also weakens the importance of species, and consequently taxinomy and systematics, and tends to separate evolution from ecology, and micro- from macro-evolution.
Authors' response: As argued above, transmission units are not actually separated from evolutionary units under our concept. On the contrary, there is a strong connection between the two. With regard to definitions of life and what most biologists will or will not call "living", we cannot bring ourselves to care. We certainly do not claim that FUEs are "alive" (or otherwise, "not alive"). They are essential units of the biological world, and that is more than enough. A recent debate on whether viruses are "alive or not" and how relevant the answer to that question is to our understanding of evolution provides a perspective on this issue [69–71].
Denying species the role of evolving units because of the existence of phylogenetic problems appears questionable to me. Species are typically defined irrespective of phylogeny. Nobody would deny Homo sapiens the species status, although we are phylogenetically the combination of two ancestral species (a proto-eukaryote and a proto-mitochondrion). The reason why we have problems defining species in prokaryotes is lack of sexual reproduction, not HGTs.
Authors' response: On this issue there seems to be no fundamental disagreement but rather a semantic one. Indeed, species can be meaningfully defined only for life forms with regular sexual reproduction and the resulting reproductive isolation (from other species). Accordingly, prokaryotes do not "really" form species . Animals certainly do form species (sensu Mayr). There is no reason to deny Homo sapiens the species status but it is useful to remember that this species goes back only some 5-6 million years not to the time of the mitochondrial symbiogenesis.
8. Unnecessary, unimportant tree of life
I would like to know more about the prevalence of HGT before adopting this conclusion (and see ref 62 for a detailed version of Vincent Daubin's and my opinion on the subject). Let me just recall that the proportion of genes whose history has been affected by HGT is not a good measure of how much HGT blurs the species tree, since this proportion will mechanically increase as you add species (and one cannot reasonably argue he knows less and less about the species tree as he includes more and more data). Imagine a data set made of 1000 genes in 10000 species, in which every gene tree is distant only a single HGT from the consensus tree. I would be happy to draw this "tree of 0%", and call it the tree of life (and use it to map and study HGT events), even though not a single gene fully agrees with it. We need better measures of the phylogenetic impact of HGT.
Authors' response: This seems to be a difference of degree not really kind. We agree that there is a central trend in the Forest of Life, and one may choose to denote it the tree of life although we are reluctant to do so. But we also know that the topologies of the trees in the FOL are highly inconsistent and that there is a substantial fraction of genes for which HGT is common . Of course, we are not going to debate the point about the need to better measure the phylogenetic impact of HGT - yes, certainly, it needs to be measured better.
Reviewer 4: William Martin, University of Duesseldorf
I'm not terribly keen on this paper. It first sets up a tree of life crisis: is the history of life shaped like a tree in the sense that Darwin envisaged or is it not because unbeknownst to Darwin different genes have different histories. It then purports to solve the tree of life crisis by conjuring up a fundamental unit of evolution (FUE) that is defined as a thing having "a substantial degree of evolutionary independence" (a very soft definition that could apply to a nucleotide or a human being, depending upon the meaning of substantial) and taken here to mean nucleotide stretches of some length. They point out that FUEs, if energetically coerced to replicate and mutate in the absence of recombination, generate tree-like structures of genealogy over time, which I think we already knew. Then they stride into the conclusions that the history of life is properly represented by the sum of all FUE-trees, giving the forest of life (the FOL), but without providing such a graphical representation or approximation thereof, and surmise that "a species or organismal tree is not a fundamental concept". My beef is this: By declaring the object of debate (an organismal tree) not to be a fundamental concept, they do not contribute to the debate, but open up a different one that detracts from the one at hand. For example, I could say "no FUE can go about its replication business without some source of energy being tapped, such that replication is not a fundamental concept, energy is the issue," but that does not help us to review this paper, it just opens up a different issue. In my view, that is what the present paper does in the context of the present debate.
Moving swiftly to the final passage of the text, with the content of which I completely disagree, we see that it says: "Darwin was entirely correct in his belief that a tree is an accurate depiction of the evolutionary process but, for obvious reasons, he was unable to correctly identify the fundamental unit of evolution." I think I can discern what the first part of that sentence means in the context of this paper, but it is only true in the absence of recombination, and the question of what the fundamental units of evolution are is distinct from what people are debating, namely is there a tree of life or is there not? Moreover, no gene-like molecule (FUE) replicates by itself, it needs a cell to do that, so that the salient argument of what the units of evolution are fails, in my view.
One aspect of the current debate is nicely summed up in a passage on page 4025 of Galtier and Daubin , where they write:
"Recently, several authors have questioned the usefulness of the species tree in prokaryote evolutionary genomics, based on the observation that only a tiny fraction (1% or less) of reconstructed gene trees are congruent with the reconstructed species tree (Dagan & Martin 2006 Bapteste et al. 2008). This, we think, is not a correct argument. In our view, the species tree could still be a useful concept even if incongruent with every gene tree, as we now discuss in more detail.
Owing to incomplete lineage sorting, roughly 30 per cent of human genes do not support the (gorilla, (human, chimpanzee)) topology (Hobbolt et al. 2007). This problem must concern other recently diverged triplets of primate species. If we think of a dataset made of 10 such triplets (plus other species), then only 3 per cent (0.710) of true gene trees will be identical to the species tree. As we add more species, and more triplets affected by incomplete lineage sorting, this percentage decreases. Does this mean that the primate species tree is useless? Obviously not."
The foregoing quote discusses prokaryote genome evolution and lineage sorting in primate gene divergence in the same breath, as if they were the same process and subject to the same mechanisms. They are not. Meiosis is different from conjugation, transduction, natural competence, gene transfer agents as in Rhodobacter, and integrons and has different consequences over geological time. Some of us are projecting our views of evolution as obtained from the study of vertebrate phylogeny, which is tree-like, onto prokaryote evolution, which is not. In doing so, we are forcing the data from prokaryotes into the conceptual straightjacket of a tree, or filtering the observations from genomes so that only those that look tree-like come to be registered for interpretation. A better distinction needs to be made in this debate between eukaryotes, which undergo reciprocal recombination, and prokaryotes, which do not.
And the present paper? The present paper calls the FOL the solution and asserts that the search for the FOL is the grail, and that "the quest for an all-encompassing tree is futile". Well, in the paper where the FOL is presented , Koonin and Wolf surmise that there is some central trend and show trees of life. I see some inconsistency there, but no matter.
Authors' response: In our opinion, no inconsistency whatever. We show trees that reflect the central trend that objectively exists in the FOL  and this is how we discuss the issue here. One may choose to call describe this central trend "a tree of life" but we at least find this more misleading than helpful given the difference from the traditional "species tree" definition.
As I see it, the current tree of life debate, whether crisis or not, is about the things that Ford Doolittle has recently summed up elsewhere . My own views on the issue are largely similar to Doolittle's and are to some extent expressed in a different paper having many authors that is also submitted to Biology Direct at this time .
Introduce New Material
Inform students of the learning targets:
- I can trace the history of the theory of evolution.
- I know that many scientists have contributed to our understanding of the current theory of evolution.
- I can identify the 5 points of Darwin’s theory of evolution.
Introduce the vocabulary associated with the lesson: adaptation, fitness, natural selection, trait, and evolution. Plan to explicitly teach the vocabulary associated with the lesson at the appropriate times within the lesson.
Read each of the following statements aloud:
- Man came from monkeys.
- Evolution happens quickly.
- Darwin was the only evolutionary theorist.
Explain that each statement will be read a 2 nd time. But, this time students should move to the side of the room labeled AGREE or DISAGREE that reflects their opinion. Note: Prior to class, post a sheet of paper labeled AGREE on one side of the room and another labeled DISAGREE on the opposite side of the room.
Instruct students to refrain from talking with one another and to move quickly to the side of the room they choose after the statement is made. This activity serves as a formative assessment of common student misconceptions about evolution. Note the number of students who affirm agreement with these statements.
After completing this activity, instruct students to return to their seats. Do not engage in a discussion about how students responded to the statements as students will have a second opportunity to respond to these same questions at the end of the lesson.
Begin instruction on the history of Evolution, part 1. Provide evolution guided notes or use a note-taking format that has been taught.
Emphasize that Darwin was not the only evolutionary theorist. Spend time discussing Lamarck’s theory and emphasize how it differs from Darwin’s theory of natural selection. Check for understanding using a visual image the evolution of the giraffe. Instruct students to look at the picture and explain how the giraffe’s neck changed. Listen to their responses as many students will wrongly identify that the giraffe somehow stretched its neck based on need. Swiftly correct this type of thinking and identify it as Lamarckism.
Help students grasp the error of Lamarckism by applying Lamarck’s concept to real-life situations. For example ask, “Can I change my height just because I want to play in the NBA?” or “If I get light brown contact lens, will my children be born with light brown eyes?”
Spend time discussing each of the 5 principles of Natural Selection. Identify each principle and then ask students to think of a good example for each principle before showing an example of each principle. This allows students to practice critical thinking skills and assess their own understanding before answers are provided for them.
Share a brief video clip on the evolution of the peppered moth to help students deepen their understanding of the process of natural selection.
Compare and contrast natural selection with artificial selection using dog breeding as a real-world example since many students will have some experience or knowledge of pure breed and mixed-breed dogs.
Instruct students to consider this question: Are there downsides to artificial selection?
Give students a moment to ponder the thought before instructing them to turn and talk for 1-2 minutes with a classmate. Walk around and listen to their comments to assess whether students are able to convey an understanding that it is not necessarily good if variance is eliminated from a dog breed because not only are favorable traits passed on but also less favorable ones, as well. End the discussion by clarifying that there can be a down side to artificial selection because the process removes variation in a population. Explain that selectively bred organisms can be especially susceptible to diseases or changes in the environment that would not be a problem for a natural selection population of organisms.
VCE Biology Unit 4: Human evolution
After the discovery of more than 500 hominin bones, scientists have realised the evolution of humankind is not as straight forward as Darwin first suggested. This clip uses a cladogram to explain a multi-branched evolutionary line as well as give a broad understanding of the species who evolved.
Where did we come from? What makes us human? This three-part series investigates dramatic new discoveries that are transforming the picture of how we became human. The first program explores fresh clues about our earliest ancestors in Africa
This second episode investigates the first skeleton that really looks like us - Turkana Boy - an astonishingly complete specimen of Homo erectus found by the famous Leakey team in Kenya.
The final episode examines the fate of the Neanderthals, our European cousins who died out as modern humans spread from Africa into Europe during the Ice Age. Did modern humans interbreed with Neanderthals or exterminate them? As for Homo sapiens, we have planet Earth to ourselves today, but that's a very recent and unusual situation. For millions of years, many kinds of hominids co-existed. The program looks at why 'we' survived while those other ancestral cousins died out