Sunday, August 23, 2009

Human eye

The human eye
1:posterior chamber 2:ora serrata 3:ciliary muscle 4:ciliary zonules 5:canal of Schlemm 6:pupil 7:anterior chamber 8:cornea 9:iris 10:lens cortex 11:lens nucleus 12:ciliary process 13:conjunctiva 14:inferior oblique muscle 15:inferior rectus muscle 16:medial rectus muscle 17:retinal arteries and veins 18:optic disc 19:dura mater 20:central retinal artery 21:central retinal vein 22:optic nerve 23:vorticose vein 24:bulbar sheath 25:macula 26:fovea 27:sclera 28:choroid 29:superior rectus muscle 30:retina

The human eye is an organ which reacts to light for several purposes.

As a conscious sense organ, the eye allows vision. Rod and cone cells in the retina allow conscious light perception and vision including color differentiation and the perception of depth. The human eye can distinguish about 10 million colors.[1]

In common with the eyes of other mammals, the human eye's non-image-forming photosensitive ganglion cells in the retina receive the light signals which affect adjustment of the size of the pupil, regulation and suppression of the hormone melatonin and entrainment of the body clock.

Contents

[hide]

[edit] General properties

The eye is not properly a sphere, rather it is a fused two-piece unit. The smaller, less curved unit called the cornea, is linked to the larger unit called the sclera. The cornea and sclera are connected by a ring called the limbus. The iris and its black center, the pupil, are seen instead of the cornea due to the cornea's transparency. To see inside the eye, the ophthalmoscope is needed, since light is not reflected out. The fundus (area opposite the pupil) shows the characteristic pale optic disk (papilla), where vessels entering the eye pass across and optic nerve fibers depart the globe.

[edit] Dimensions

The dimensions differ among adults by only one or two millimeters. The vertical measure, generally less than the horizontal distance, is about 24 mm among adults, at birth about 16-17 mm. The eyeball grows rapidly, increasing to 22.5-23 mm (approx. 0.89 in) by the age of three years. From then to age 13, the eye attains its full size. The volume is 6.5 ml (0.4 cu. in.) and the weight is 7.5 g. (0.25 oz.)

[edit] Components

The eye is made up of three coats, enclosing three transparent structures. The outermost layer is composed of the cornea and sclera. The middle layer consists of the choroid, ciliary body, and iris. The innermost is the retina, which gets its circulation from the vessels of the choroid as well as the retinal vessels, which can be seen in an opthalmoscope.

Within these coats are the aqueous humor, the vitreous body, and the flexible lens. The aqueous humor is a clear fluid that is contained in two areas: the anterior chamber between the cornea and the iris and exposed area of the lens; and the posterior chamber, behind the iris and the rest. The lens is suspended to the ciliary body by the suspensory ligament (Zonule of Zinn), made up of fine transparent fibers. The vitreous body is a clear jelly that is much larger than the aqueous humor, and is bordered by the sclera, zonule, and lens. They are connected via the pupil. [2]

[edit] Dynamic range

The retina has a static contrast ratio of around 100:1 (about 6 1/2 f-stops). As soon as the eye moves (saccades) it re-adjusts its exposure both chemically and by adjusting the iris. Initial dark adaptation takes place in approximately four seconds[citation needed] of profound, uninterrupted darkness; full adaptation through adjustments in retinal chemistry (the Purkinje effect) are mostly complete in thirty minutes[citation needed]. Hence, a dynamic contrast ratio of about 1,000,000:1 (about 20 f-stops) is possible. The process is nonlinear and multifaceted, so an interruption by light merely starts the adaptation process over again. Full adaptation is dependent on good blood flow; thus dark adaptation may be hampered by poor circulation, and vasoconstrictors like alcohol or tobacco.

The eye includes a lens not dissimilar to lenses found in optical instruments such as cameras and the same principles can be applied. The pupil of the human eye is its aperture; the iris is the diaphragm that serves as the aperture stop. Refraction in the cornea causes the effective aperture (the entrance pupil) to differ slightly from the physical pupil diameter. The entrance pupil is typically about 4 mm in diameter, although it can range from 2 mm (f/8.3) in a brightly lit place to 8 mm (f/2.1) in the dark.

[edit] Field of view

The approximate field of view of a human eye is 95° Out, 75° Down, 60° In, 60° Up. About 12-15° temporal and 1.5° below the horizontal is the optic nerve or blind spot which is roughly 7.5° in height and 5.5° in width.[citation needed]

[edit] Eye irritation

Eye irritation is a common problem experienced by people of all ages. There are numerous causes in which some can be prevented and treated properly. However, in order to take precaution it is important to have some basic knowledge regarding what eye irritants are and where they can be found in our environments. Eye irritation depends somewhat on destabilization of the outer-eye tear film. Certain volatile organic compounds that are both chemically reactive and airway irritants may cause eye irritation as well. Personal factors (eg, use of contact lenses, eye make-up, and certain medication) may also affect destabilization of the tear film and possibly result in more eye symptoms [3]. Nevertheless, if airborne particles alone should destabilize the tear film and cause eye irritation, their content of surface-active compounds must be high [3]. An integrated physiological risk model with blink frequency, destabilization, and break-up of the eye tear film as inseparable phenomena may explain eye irritation among office workers in terms of occupational, climate, and eye-related physiological risk factors [3].

In a study conducted by NIOSH, the frequency of reported symptoms in industrial buildings was investigated[citation needed] [4]. The study's results were that eye irritation was the most frequent symptom in industrial building spaces, at 81%. Modern office work with use of office equipment has raised concerns about possible adverse health effects [5]. Since the 1970s, reports have linked mucosal, skin, and general symptoms to work with self-copying paper. Emission of various particulate and volatile substances has been suggested as specific causes. These symptoms have been related to Sick Building Syndrome, which involves symptoms such as irritation to the eyes, skin, and upper airways, headache and fatigue [6].

Many of the symptoms described in Sick Building Syndrome (SBS) and multiple chemical sensitivity (MCS) resemble the symptoms known to be elicited by airborne irritant chemicals [7]. A repeated measurement design was employed in the study of acute symptoms of eye and respiratory tract irritation resulting from occupational exposure to sodium borate dusts [8]. The symptom assessment of the 79 exposed and 27 unexposed subjects comprised interviews before the shift began and then at regular hourly intervals for the next six hours of the shift, four days in a row [8]. Exposures were monitored concurrently with a personal real time aerosol monitor. Two different exposure profiles, a daily average and short term (15 minute) average, were used in the analysis. Exposure-response relations were evaluated by linking incidence rates for each symptom with categories of exposure [8].

Acute incidence rates for nasal, eye, and throat irritation, and coughing and breathlessness were found to be associated with increased exposure levels of both exposure indices. Steeper exposure-response slopes were seen when short term exposure concentrations were used. Results from multivariate logistic regression analysis suggest that current smokers tended to be less sensitive to the exposure to airborne sodium borate dust [8].

[edit] Eye movement

MRI scan of human eye

The visual system in the brain is too slow to process information if the images are slipping across the retina at more than a few degrees per second.[9] Thus, for humans to be able to see while moving, the brain must compensate for the motion of the head by turning the eyes. Another complication for vision in frontal-eyed animals is the development of a small area of the retina with a very high visual acuity. This area is called the fovea, and covers about 2 degrees of visual angle in people. To get a clear view of the world, the brain must turn the eyes so that the image of the object of regard falls on the fovea. Eye movements are thus very important for visual perception, and any failure to make them correctly can lead to serious visual disabilities.

Having two eyes is an added complication, because the brain must point both of them accurately enough that the object of regard falls on corresponding points of the two retinas; otherwise, double vision would occur. The movements of different body parts are controlled by striated muscles acting around joints. The movements of the eye are no exception, but they have special advantages not shared by skeletal muscles and joints, and so are considerably different.

[edit] Extraocular muscles

Each eye has six muscles that control its movements: the lateral rectus, the medial rectus, the inferior rectus, the superior rectus, the inferior oblique, and the superior oblique. When the muscles exert different tensions, a torque is exerted on the globe that causes it to turn, in almost pure rotation, with only about one millimeter of translation.[10] Thus, the eye can be considered as undergoing rotations about a single point in the center of the eye.

[edit] Rapid eye movement

Rapid eye movement, or REM for short, typically refers to the sleep stage during which the most vivid dreams occur. During this stage, the eyes move rapidly. It is not in itself a unique form of eye movement.

[edit] Saccades

Saccades are quick, simultaneous movements of both eyes in the same direction controlled by the frontal lobe of the brain. Some irregular drifts, movements, smaller than a cascade and larger than a microscopical, subtend up to six minutes of arc.

[edit] Microsaccades

Even when looking intently at a single spot, the eyes drift around. This ensures that individual photosensitive cells are continually stimulated in different degrees. Without changing input, these cells would otherwise stop generating output. Microsaccades move the eye no more than a total of 0.2° in adult humans.

[edit] Vestibulo-ocular reflex

The vestibulo-ocular reflex is a reflex eye movement that stabilizes images on the retina during head movement by producing an eye movement in the direction opposite to head movement, thus preserving the image on the center of the visual field. For example, when the head moves to the right, the eyes move to the left, and vice versa.

[edit] Smooth pursuit movement

The eyes can also follow a moving object around. This tracking is less accurate than the vestibulo-ocular reflex, as it requires the brain to process incoming visual information and supply feedback. Following an object moving at constant speed is relatively easy, though the eyes will often make saccadic jerks to keep up. The smooth pursuit movement can move the eye at up to 100°/s in adult humans.

It is more difficult to visually estimate speed in low light conditions or while moving, unless there is another point of reference for determining speed.

[edit] Optokinetic reflex

The optokinetic reflex is a combination of a saccade and smooth pursuit movement. When, for example, looking out of the window at a moving train, the eyes can focus on a 'moving' train for a short moment (through smooth pursuit), until the train moves out of the field of vision. At this point, the optokinetic reflex kicks in, and moves the eye back to the point where it first saw the train (through a saccade).

[edit] Vergence movement

The two eyes converge to point to the same object.

When a creature with binocular vision looks at an object, the eyes must rotate around a vertical axis so that the projection of the image is in the centre of the retina in both eyes. To look at an object closer by, the eyes rotate 'towards each other' (convergence), while for an object farther away they rotate 'away from each other' (divergence). Exaggerated convergence is called cross eyed viewing (focusing on the nose for example) . When looking into the distance, or when 'staring into nothingness', the eyes neither converge nor diverge.

Vergence movements are closely connected to accommodation of the eye. Under normal conditions, changing the focus of the eyes to look at an object at a different distance will automatically cause vergence and accommodation.

There are many diseases, disorders, and age-related changes that may affect the eyes and surrounding structures.

As the eye ages certain changes occur that can be attributed solely to the aging process. Most of these anatomic and physiologic processes follow a gradual decline. With aging, the quality of vision worsens due to reasons independent of aging eye diseases. While there are many changes of significance in the nondiseased eye, the most functionally important changes seem to be a reduction in pupil size and the loss of accommodation or focusing capability (presbyopia). The area of the pupil governs the amount of light that can reach the retina. The extent to which the pupil dilates also decreases with age. Because of the smaller pupil size, older eyes receive much less light at the retina. In comparison to younger people, it is as though older persons wear medium-density sunglasses in bright light and extremely dark glasses in dim light. Therefore, for any detailed visually guided tasks on which performance varies with illumination, older persons require extra lighting. Certain ocular diseases can come from sexually transmitted diseases such as herpes and genital warts. If contact between eye and area of infection occurs, the STD can be transmitted to the eye.[11]

With aging a prominent white ring develops in the periphery of the cornea- called arcus senilis. Aging causes laxity and downward shift of eyelid tissues and atrophy of the orbital fat. These changes contribute to the etiology of several eyelid disorders such as ectropion, entropion, dermatochalasis, and ptosis. The vitreous gel undergoes liquefaction (posterior vitreous detachment or PVD) and its opacities — visible as floaters — gradually increase in number.

Various eye care professionals, including ophthalmologists, optometrists, and opticians, are involved in the treatment and management of ocular and vision disorders. A Snellen chart is one type of eye chart used to measure visual acuity. At the conclusion of an eye examination, an eye doctor may provide the patient with an eyeglass prescription for corrective lenses. Some disorders of the eyes for which corrective lenses are prescribed include myopia (near-sightedness) which affects one-third of the population, hyperopia (far-sightedness) which affects one quarter of the population, and presbyopia, a loss of focusing range due to aging.

[edit] See also

Thursday, August 20, 2009

definition of excretion

The elimination by an organism of waste products that result from metabolic processes. In plants, waste is minimal and is eliminated primarily by diffusion to the outside environment. Animals have specific organs of excretion. In vertebrates, the kidney filters blood, conserving water and producing urea and other waste products in the form of urine. The urine is then passed through the ureters to the bladder and discharged through the urethra. The skin and lungs, which eliminate carbon dioxide, are also excretory organs.

nutrition and excretion

Plant Water Relations

The study of world of life is as old as man itself. All living organisms are made up of a few elements which are repeated in each of them. The basic unit of life - cell, is a structural and functional entity of life.

Plant Nutrition

The plants upon which we depend for the food we eat, and for the oxygen we breathe, depend in turn upon the soil. A good soil supplies the plants with the mineral elements they use. Vigorous, highly productive plants can be grown in solutions of fertilizer minerals in the absence of soil.

Photosynthesis

The first photosynthetic organism probably appeared almost three billion years ago. With the evolution of photosynthesis, however, organisms began to change the face of our planet and, as a consequence, to exert strong influences on each other. Organisms have continued to change the environment, at an ever increasing rate, up to the present day.

Respiration

All living organisms require a continuous supply of energy for carrying out various functions. The main source of energy for all the functions, in all living organisms is cellular respiration.

Animal Nutrition

Nutrition can be defined as the process by which an organism obtains food which is used to provide energy and materials for its life sustaining activities.

Respiration in Animals

All living creatures need food. The food is consumed so that energy is obtained. The energy is utilised by the body for various purposes like locomotion, conduction of impulses, repair of damaged tissues, building of cell materials, etc.

Circulation in Animals

Materials formed in one part of the body have to be taken up to other parts where they are needed or to be got rid of. This is an essential requirement of most animals. This function is performed by the body fluids.

Osmoregulation and Excretion in Animals

The nitrogenous waste materials produced in the animal body due to metabolic reactions are of no use to the cell. These waste materials if allowed to accumulate in the body, may become toxic. Therefore, they must be removed from the body. The process of elimination of metabolic waster products from the animal body to regulate the composition of the body fluids and tissues is called excretion.

Movement and Locomotion in Animals

The act of changing place or position by the entire body or by one or more of its parts is called movement. Movement is one of the characteristic features of living organisms. Study of movements is called kinesiology.

Nervous Coordination and Integration in Animals

Animals are different from plants because of their ability of locomotion. This ability probably developed as they have to search for food, unlike the plants that are autotrophic. Since they move from place to place, the animals have to continuously encounter changes in their environment. All animals, in order to maintain a steady state within the body (homeostasis), should be able to perceive these changes and adapt to them.

Chemical Coordination in Animals

A cell, a tissue or an organ, which secretes certain useful chemical compounds required for a particular function, is called a Gland.

Reproduction in Flowering Plants

The creation of a life form, by a similar life is called reproduction. Reproduction is the extension of life of a species at a given time. It is a means of perpetuation of the species and also multiplies their number. By this process, the individuals transmit life to the next generation and thereby ensure the continued existence of living organisms on earth. If there was no reproduction, life on this earth would sooner or later come to an end.

Plant Growth and Movements

The term growth is applied to several things and situations. It is quite common to hear people referring to growth of cities, the weeds, of tradition or even of indiscipline. You would have observed the growth of crystals or salt in the laboratory, but it is of non-living things.

Reproduction and Development in Animals

An animal performs all its life functions with an aim to be alive till it matures and reproduces. Reproduction is the ability of living organisms to produce new individuals similar to themselves. Reproduction ensures perpetuation and survival of their species. It leads to an increase in the number of individuals of a species when conditions are favourable.

Growth, Regeneration and Ageing

Growth is defined as an increase in the size and weight of an organism due to synthesis of new protoplasm.

Organisms and the Environment

he term ecology is derived from two Greek words (oikos - means 'house' or place to live and logos means 'a discussion or study'). Literally, ecology is the study of organism 'at home' in their native environment. The term was first introduced by Reiter in 1868, but was fully defined by Ernest Haeckel in 1869.

Population, Biotic Community and Succession

Biotic community is an association of a number of interrelated and independent populations belonging to different species, in a common environment which can survive in nature.

Ecosystem Structure and Function

Biogeography reveals that living organisms (plants and animals) are found practically everywhere on this earth. The living components interact among themselves as well as with their physical environment like soil, air and water.

Natural Resources and their Conservation

The term 'natural resources' refers to all the natural things on our earth. It includes everything, that is naturally available and that is not creatable by any human activity. It specifically excludes the materials created by man.

Biodiversity

The word 'resource' means supplying a material generally held in reserve. The common natural resources include energy, air, water, land, minerals, microorganisms plants and animals.

Environmental Pollution

It is aptly said that pollution is the price paid by us towards social development through scientific advancement. Pollution is a peril of our society. It is a peril out of scientific achievements applied to improvement of human facilities.

Global Environmental Changes

The atmosphere resource of our world is unique and available to our planet only. No other planet is found to have similar atmosphere. Earth's atmosphere is a legacy from history of this planet. It was formed billions of years back. In the formative years, as the earth started cooling, it did not have free oxygen (theory of chemical evolution by Oparin and Haldane). The atmosphere, lithosphere and hydrosphere were not clearly distinguishable. As micromolecules and macromolecules of C, H, N and O compounds like, glycerol, fat, pyrimidines, polysaccharide, lipid, proteins, nucleic acids were formed, the life forms originated.

Human Population and Health

Although population of some animals is also studied, the population of human beings is most extensively studied. Whenever the word population is used, it connotes the human population. Population is one of the most important subjects known for having large scale ramifications on economic, social, environmental and developmental scenario of a country.

Food Production

One of the primary objectives of agriculture is to produce food. In the entire history of agriculture, food production has remained a prime objective.

Immune System and Human Health

Living organisms are exposed to various external or foreign substances and disease causing organisms like bacteria, viruses and fungi. Such organisms which can cause a disease are known as Pathogens. It is observed that some human beings are more prone to a certain disease and some others are immune to it.

Biomedical Technologies

Doctors use a number of simple instruments like thermometer to monitor body temperature of patients, stethoscope to listen to heart sounds, BP instrument to check the blood pressure, BP instrument to check the blood pressure and so on. But today technology has revolutionised the world of medicine and the tools used for diagnosis of diseases.

InnerBody.com Logo

Biological classification

Biological classification or scientific classification in biology, is a method by which biologists group and categorize organisms by biological type, such as genus or species. Biological classification is a form of scientific taxonomy, but should be distinguished from folk taxonomy, which lacks scientific basis. Modern biological classification has its root in the work of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings since have been revised to improve consistency with the Darwinian principle of common descent. Molecular phylogenetics, which uses DNA sequences as data, has driven many recent revisions and is likely to continue to do so. Biological classification belongs to the science of biological systematics.

Contents

[hide]

[edit] Early systems

[edit] Ancient through medieval times

Current systems of classifying forms of life descend from the thought presented by the Greek philosopher Aristotle, who published in his metaphysical and logical works the first known classification of everything whatsoever, or "being". This is the scheme that gave such words as 'substance', 'species' and 'genus' and was retained in modified and less general form by Linnaeus.

Aristotle also studied animals and classified them according to method of reproduction, as did Linnaeus later with plants. Aristotle's animal classification was soon made obsolete by additional knowledge and was forgotten.

The philosophical classification is in brief as follows.[1] Primary substance is the individual being; for example, Peter, Paul, etc. Secondary substance is a predicate that can properly or characteristically be said of a class of primary substances; for example, man of Peter, Paul, etc. The characteristic must not be merely in the individual; for example, being skilled in grammar. Grammatical skill leaves most of Peter out and therefore is not characteristic of him. Similarly man (all of mankind) is not in Peter; rather, he is in man.

Species is the secondary substance that is most proper to its individuals. The most characteristic thing that can be said of Peter is that Peter is a man. An identity is being postulated: "man" is equal to all its individuals and only those individuals. Members of a species differ only in number but are totally the same type.

Genus is a secondary substance less characteristic of and more general than the species; for example, man is an animal. Not all animals are men. It is clear that a genus contains species. There is no limit to the number of Aristotelian genera that might be found to contain the species. Aristotle does not structure the genera into phylum, class, etc., as the Linnaean classification does.

The secondary substance that distinguishes one species from another within a genus is the specific difference. Man can thus be comprehended as the sum of specific differences (the "differentiae" of biology) in less and less general categories. This sum is the definition; for example, man is an animate, sensate, rational substance. The most characteristic definition contains the species and the next most general genus: man is a rational animal. Definition is thus based on the unity problem: the species is but one yet has many differentiae.

The very top genera are the categories. There are ten: one of substance and nine of "accidents", universals that must be "in" a substance. Substances exist by themselves; accidents are only in them: quantity, quality, etc. There is no higher category, "being", because of the following problem, which was only solved in the Middle Ages by Thomas Aquinas: a specific difference is not characteristic of its genus. If man is a rational animal, then rationality is not a property of animals. Substance therefore cannot be kind of being because it can have no specific difference, which would have to be non-being.

The problem of being occupied the attention of scholastics during the time of the Middle Ages. The solution of St. Thomas, termed the analogy of being, established the field of ontology, which received the better part of the publicity and also drew the line between philosophy and experimental science. The latter rose in the Renaissance from practical technique. Linnaeus, a classical scholar, combined the two on the threshold of the neo-classicist revival now called the Age of Enlightenment.

[edit] Renaissance through age of reason

An important advance was made by the Swiss professor, Conrad von Gesner (1516–1565). Gesner's work was a critical compilation of life known at the time.

The exploration of parts of the New World produced large numbers of new plants and animals that needed descriptions and classification. The old systems made it difficult to study and locate all these new specimens within a collection and often the same plants or animals were given different names simply because there were too many species to keep track of. A system was needed that could group these specimens together so they could be found; the binomial system was developed based on morphology with groups having similar appearances. In the latter part of the 16th century and the beginning of the 17th, careful study of animals commenced, which, directed first to familiar kinds, was gradually extended until it formed a sufficient body of knowledge to serve as an anatomical basis for classification. Advances in using this knowledge to classify living beings bear a debt to the research of medical anatomists, such as Fabricius (1537–1619), Petrus Severinus (1580–1656), William Harvey (1578–1657), and Edward Tyson (1649–1708). Advances in classification due to the work of entomologists and the first microscopists is due to the research of people like Marcello Malpighi (1628–1694), Jan Swammerdam (1637–1680), and Robert Hooke (1635–1702). Lord Monboddo (1714–1799) was one of the early abstract thinkers whose works illustrate knowledge of species relationships and who foreshadowed the theory of evolution. Successive developments in the history of insect classification may be followed on the website[2] by clicking on succeeding works in chronological order.

[edit] Early methodists

Since late in the 15th century, a number of authors had become concerned with what they called methodus, (method). By method authors mean an arrangement of minerals, plants, and animals according to the principles of logical division. The term Methodists was coined by Carolus Linnaeus in his Bibliotheca Botanica to denote the authors who care about the principles of classification (in contrast to the mere collectors who are concerned primarily with the description of plants paying little or no attention to their arrangement into genera, etc). Important early Methodists were Italian philosopher, physician, and botanist Andrea Caesalpino, English naturalist John Ray, German physician and botanist Augustus Quirinus Rivinus, and French physician, botanist, and traveller Joseph Pitton de Tournefort.

Andrea Caesalpino (1519–1603) in his De plantis libri XVI (1583) proposed the first methodical arrangement of plants. On the basis of the structure of trunk and fructification he divided plants into fifteen "higher genera".

John Ray (1627–1705) was an English naturalist who published important works on plants, animals, and natural theology. The approach he took to the classification of plants in his Historia Plantarum was an important step towards modern taxonomy. Ray rejected the system of dichotomous division by which species were classified according to a pre-conceived, either/or type system, and instead classified plants according to similarities and differences that emerged from observation.

Both Caesalpino and Ray used traditional plant names and thus, the name of a plant did not reflect its taxonomic position (e.g. even though the apple and the peach belonged to different "higher genera" of John Ray's methodus, both retained their traditional names Malus and Malus Persica respectively). A further step was taken by Rivinus and Pitton de Tournefort who made genus a distinct rank within taxonomic hierarchy and introduced the practice of naming the plants according to their genera.

Augustus Quirinus Rivinus (1652–1723), in his classification of plants based on the characters of the flower, introduced the category of order (corresponding to the "higher" genera of John Ray and Andrea Caesalpino). He was the first to abolish the ancient division of plants into herbs and trees and insisted that the true method of division should be based on the parts of the fructification alone. Rivinus extensively used dichotomous keys to define both orders and genera. His method of naming plant species resembled that of Joseph Pitton de Tournefort. The names of all plants belonging to the same genus should begin with the same word (generic name). In the genera containing more than one species the first species was named with generic name only, while the second, etc were named with a combination of the generic name and a modifier (differentia specifica).

Joseph Pitton de Tournefort (1656–1708) introduced an even more sophisticated hierarchy of class, section, genus, and species. He was the first to use consistently the uniformly composed species names that consisted of a generic name and a many-worded diagnostic phrase differentia specifica. Unlike Rivinus, he used differentiae with all species of polytypic genera.

[edit] Modern systems

[edit] Linnaean

Carolus Linnaeus' great work, the Systema Naturae (1st ed. 1735), ran through twelve editions during his lifetime. In this work, nature was divided into three kingdoms: mineral, vegetable and animal. Linnaeus used five ranks: class, order, genus, species, and variety.

He abandoned long descriptive names of classes and orders and two-word generic names (e. g. Bursa pastoris) still used by his immediate predecessors (Rivinus and Pitton de Tournefort) and replaced them with single-word names, provided genera with detailed diagnoses (characteres naturales), and reduced numerous varieties to their species, thus saving botany from the chaos of new forms produced by horticulturalists.

Linnaeus is best known for his introduction of the method still used to formulate the scientific name of every species. Before Linnaeus, long many-worded names (composed of a generic name and a differentia specifica) had been used, but as these names gave a description of the species, they were not fixed. In his Philosophia Botanica (1751) Linnaeus took every effort to improve the composition and reduce the length of the many-worded names by abolishing unnecessary rhetorics, introducing new descriptive terms and defining their meaning with an unprecedented precision. In the late 1740s Linnaeus began to use a parallel system of naming species with nomina trivialia. Nomen triviale, a trivial name, was a single- or two-word epithet placed on the margin of the page next to the many-worded "scientific" name. The only rules Linnaeus applied to them was that the trivial names should be short, unique within a given genus, and that they should not be changed. Linnaeus consistently applied nomina trivialia to the species of plants in Species Plantarum (1st edn. 1753) and to the species of animals in the 10th edition of Systema Naturae (1758).

By consistently using these specific epithets, Linnaeus separated nomenclature from taxonomy. Even though the parallel use of nomina trivialia and many-worded descriptive names continued until late in the eighteenth century, it was gradually replaced by the practice of using shorter proper names combined of the generic name and the trivial name of the species. In the nineteenth century, this new practice was codified in the first Rules and Laws of Nomenclature, and the 1st edn. of Species Plantarum and the 10th edn. of Systema Naturae were chosen as starting points for the Botanical and Zoological Nomenclature respectively. This convention for naming species is referred to as binomial nomenclature.

Today, nomenclature is regulated by Nomenclature Codes, which allows names divided into taxonomic ranks.

[edit] Taxonomic ranks

There are 8 main taxonomic ranks: domain, kingdom, phylum, class, order, family, genus, species.

There are slightly different ranks for zoology and for botany.

[edit] Evolutionary

Whereas Linnaeus classified for ease of identification, it is now generally accepted that classification should reflect the Darwinian principle of common descent.

Since the 1960s a trend called cladistic taxonomy (or cladistics or cladism) has emerged, arranging taxa in an evolutionary tree. If a taxon includes all the descendants of some ancestral form, it is called monophyletic, as opposed to paraphyletic. Other groups are called polyphyletic.

A new formal code of nomenclature, the International Code of Phylogenetic Nomenclature, or PhyloCode for short, is currently under development, intended to deal with names of clades. Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes.

Domains are a relatively new grouping. The three-domain system was first invented in 1990, but not generally accepted until later. Now, the majority of biologists accept the domain system, but a large minority use the five-kingdom method. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera). Consequently, the three domains of life are conceptualized as Archaea, Bacteria, and Eukaryota (comprising the nuclei-bearing eukaryotes).[3] A small minority of scientists add Archaea as a sixth kingdom, but do not accept the domain method.

Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade that groups together the Archaea and Eukarya, would have evolved from Bacteria, more precisely from Actinobacteria.


Linnaeus
1735
2 kingdoms
Haeckel
1866[4]
3 kingdoms
Chatton
1937[5]
2 empires
Copeland
1956[6]
4 kingdoms
Whittaker
1969[7]
5 kingdoms
Woese et al.
1977[8]
6 kingdoms
Woese et al.
1990[9]
3 domains
(not treated) Protista Prokaryota Monera Monera Eubacteria Bacteria
Archaebacteria Archaea
Eukaryota Protista Protista Protista Eukarya
Vegetabilia Plantae Fungi Fungi
Plantae Plantae Plantae
Animalia Animalia Animalia Animalia Animalia


[edit] Authorities (author citation)

The name of any taxon may be followed by the "authority" for the name, that is, the name of the author who first published a valid description of it. These names are frequently abbreviated: the abbreviation "L." is universally accepted for Linnaeus, and in botany there is a regulated list of standard abbreviations (see list of botanists by author abbreviation). The system for assigning authorities is slightly different in different branches of biology: see author citation (botany) and author citation (zoology). However, it is standard that if a name or placement has been changed since the original description, the first authority's name is placed in parentheses and the authority for the new name or placement may be placed after it (usually only in botany).

[edit] Globally Unique Identifiers for Names

There is a movement within the biodiversity informatics community to provide Globally Unique Identifiers in the form of Life Science Identifiers (LSID) for all biological names. This would allow authors to cite names unambiguously in electronic media and reduce the significance of errors in the spelling of names or the abbreviation of authority names. Three large nomenclatural databases (referred to as nomenclators) have already begun this process, these are Index Fungorum, International Plant Names Index and Zoo Bank. Other databases, that publish taxonomic rather than nomenclatural data, have also started using LSIDs to identify taxa. The key example of this is Catalogue of Life. The next step in integration will be when these taxonomic databases include references to the nomenclatural databases using LSIDs.

Life: Early Cells, Classification of Life

  • evolution of cells
  • earliest cells
  • prokaryotic cells
  • eukaryotic cells
  • classification of life

Evolution of early cells

  • Theories about evolution of cells
  • evolution of cells
  • early organic molecules assembled into functional, independent units
    • cells are "bags of fluid"
    • contents differed from environment outside "cell"
    • interior had a higher concentration of specific organic molecules
  • how did "bags of fluid" evolve from simple organic molecules?
  • bubbles
    • spherical, hollow structures
    • molecules with hydrophobic regions spontaneously form bubbles in water
    • structure shields hydrophobic regions from contact with water

The Earliest Cells

  • Earliest evidence of life appears in microfossils
  • dating from ~3.5 billion years ago
  • Characteristics of earliest life forms
  • small (1-2 nanometers)
  • single-celled
  • no external appendages
  • little internal structure
  • no nucleus
  • resembled today’s bacteria
  • in group called prokaryotes ("before nucleus")
  • Bacteria
  • divided into two groups
  • archaebacteria
  • eubacteria

Prokaryotic versus eukaryotic cells

  • All life
  • two types of cells
  • prokaryotic cells
  • eukaryotic cells

Prokaryotic cells are small and structurally simple

  • Prokaryotic cells
  • first appeared ~ 3.5 billion years ago
  • "before nucleus"
  • small, ~1/10th size of eukaryotic cells
  • lack true, membrane-bound nucleus
  • surrounded by plasma membrane
  • lack true, membrane-bound organelles
  • less complex than eukaryotic
  • contain a simple DNA molecule

The First Eukaryotic Cells

  • Eukaryotic cells
  • first appeared ~ 1.5 billion years ago
  • "true nucleus"
  • larger than prokaryotic
  • rapidly evolved to produce diverse life forms that inhabit earth today
  • complex interiors
  • complex interior organization
  • extensive compartmentalization
  • many membrane-bound organelles, internal membranes
  • true, membrane-bound nucleus
  • complex DNA molecule
  • contain vesicles and vacuoles which function in storage and transport

The eukaryotic cell probably originated as a community of prokaryotes

  • fossil record indicates
  • eukaryotes evolved from prokaryotes ~1.5 BYA
  • how did eukaryoites arise?
  • theory: through a combination of 2 processes
  • membrane infolding
  • endosymbiosis
  • membrane infolding
  • of plasma membrane of ancestral prokaryotic cells
  • gave rise to endomembrane system of eukaryotic cells
  • endosymbiosis
  • thought to have generated first
  • mitochondira
    • heterotrophic prokaryote came to reside in ancestral prokaryote
  • chloroplast
    • photosynthetic prokaryote came to reside in ancestral prokaryote
  • Endosymbiont theory
  • critical stage in evolution of eukaryotic cells involved symbiotic relationships with prokaryotic organisms (bacteria)
  • heterotrophic bacteria engulfed by larger bacteria - evolved into mitochondria
  • photosynthetic bacteria engulfed by larger bacteria - evolved into chloroplasts
  • Support for the endosymbiont theory
  • existence of symbiotic relationships
  • presence of DNA in organelles
  • many organelles have their own DNA
    • mitochondria
    • chloroplasts
  • organelle DNA is similar to bacterial DNA in size and character

Figure- A model of the origin of eukaryotes

Classification of Life

  • diversity of life can be arranged into three domains
  • how we classify life
  • therefore, organisms
  • To bring order to diversity of life, a system of classification exists
  • Taxonomy
  • science of classifying and naming organisms
  • earliest classification schemes
  • only two broad groups recognized (kingdoms)
  • as knowledge increased about significant differences among living organisms
  • classification system was developed that recognized a taxonomic level higher than kingdom
  • domain
  • All life can be classified into one of
  • three domains
    • Archaea
    • Bacteria
    • Eukarya
  • Domain Archaea
  • single-celled, "ancient" bacteria
  • Domain Bacteria
  • single-celled, "true" bacteria
  • Domain Eukarya
  • single-celled protists, paramecia, single- and multi-cellular algae
  • fungi
  • plants
  • animals

  • All organisms are grouped into a few major categories
  • earliest classification systems recognized 2 kingdoms of life
  • animal kingdom
  • plant kingdom
  • kingdoms were added over time
  • new organisms were discovered
  • understanding of relationships/differences grew
  • How many kingdoms?
  • all "life" currently classified into 6 kingdoms
  • Archaebacteria
  • Eubacteria
  • Protista
  • Fungi
  • Plantae
  • Animalia

Six Kingdoms Relative to 3 Domains:

  • Domain Archaea
  • Kingdom Archaebcateria
  • Domain Bacteria
  • Kingdom Eubacteria
  • Domain Eukarya
  • Kingdom Protista
  • Kingdom Fungi
  • Kingdom Plantae
  • Kingdom Animalia

Six Kingdoms Relative to Prokaryotic Versus Eukaryotic Cells:

  • Prokaryotic kingdoms
  • Archaebacteria
  • Eubacteria
  • Eukaryotic kingdoms
  • Protista
  • Fungi
  • Plantae
  • Animalia

Figure - Three domains of life

Classification of Life

  • binomial system
  • early
  • developed by Swedish biologist, Carl Linnaeus (1707-1778)
    • gave two-part (binomial) name to each species
    • names eventually came to be written in Latin
  • current
  • unique 2-part name for each organism
  • first part designates genus
    • capitalized
    • underlined or italicized in print
  • second part designates species
    • not capitalized
    • underlined or italicized in print
  • Examples
  • Homo sapiens or H. sapiens (human)
  • Quercus alba or Q. alba (white oak)

Taxonomic Classification is Hierarchical

  • taxonomic heirarchy
  • over time, genera were grouped into large, more inclusive categories known as families
  • grouping intended to reflect relationships between genera included
  • taxonomic system extended to include several, more inclusive units
  • Species
  • grouped to form a genus
  • Genera (plural of genus)
  • grouped together to form a family
  • Families
  • grouped to form orders
  • Orders
  • grouped to form classes
  • Classes
  • grouped to form divisions or phyla
  • Phyla or Divisions
  • grouped into kingdoms

Classification of the Human Being

  • Domain: Eukarya
  • Kingdom: Animalia
  • Phylum: Chordata
  • Class: Mammalia
  • Order: Primates
  • Family: Hominidae
  • Genus: Homo
  • Species: sapiens

Figure - Classifying life