Philo Judeaus


Philo Judeaus

Philo Judeaus

Philo Judeaus, also known as Philo of Alexandria, was a Jewish philosopher born in Hellenic Alexandria, Egypt. His writings are a unique blend of Greek philosophy and Jewish teachings and are the only surviving manuscripts from the culture of Hellenistic Judaism. Philo’s work reflects a deep concern with time and the meaning of life.

Philo’s writing gives much insight into the experience of the Jews within the Roman world. He was a contemporary of Jesus of Nazareth but makes no mention of Jesus in his work. Philo does discuss Pontius Pilate, the Roman governor of Judea, as well as the Roman emperors Augustus, Tiberius, Gaius Caligula, and Claudius.

Around 40 CE Philo was chosen by the Jews of Alexandria to lead a delegation to Rome to protest injustices committed against them. Philo was highly regarded within his community because of the wisdom and knowledge, as expressed in his extensive philosophical writings.

Gaius Caligula

Gaius Caligula

Little is known about the private life of Philo. Scholars believe he was born around 20 BCE to a wealthy and influential family in Alexandria. He later wrote negatively about affluence. Philo most likely received a traditional Jewish education as well as schooling in the writings of the Greeks.

His writing shows the influences of Plato, Aristotle, and the philosophies of stoicism and cynicism. Philo’s work can be divided into three general categories:

  1. discussions of Jewish law,
  2. popular works, and
  3. philosophical essays.

The discussions of Jewish law include Philo’s Allegorical Commentary on Genesis, an interpretation of the Ten Commandments and the lives of the prophets.

Jewish law

Jewish law

Popular works include the Life of Moses, intended for a wider audience. Philosophical essays consist of treatises on a variety of issues, such as On Providence and On Animals. Philo believed that the Torah contains both literal and allegorical meaning.

The Temple of Jerusalem still stood during Philo’s lifetime and had great meaning to him. He made at least one pilgrimage there. He believed that Gentiles could not be excluded from Judaism and that Jewish teachings had universal application.

Philo never departed from his strongly held Jewish beliefs, and he often serves as a bridge between the ideas of the Jews and the Greeks. Clearly the teachings of both the Jews and the Greeks have had a profound impact on the development of knowledge over time. Both schools of thought deal with the nature of humankind and its place in the universe. Philo’s work stands as the most important link between the two.

universal application

universal application

The Jewish historian Josephus wrote an account of the delegation to Rome led by Philo. The emperor Caligula had ordered statues of himself as a god erected in the Jewish temples of Alexandria.

The Jews naturally viewed this as a deliberate provocation. Philo met with Caligula directly, but the two did not find common ground. Scholars place the date of Philo’s death around 50 CE.

Philoponus and Simplicius


Philoponus and Simplicius

Philoponus and Simplicius

The beginning or the eternity of the world and infinity or finitude of time is a central topic in the philosophy of late antiquity, especially in the debate between Christians and pagans.

This quarrel started for the first time in the Neoplatonic school of Alexandria in the 6th century CE between John Philoponus and Simplicius, who were the philosophically most talented pupils of Ammonius Hermeiou. Simplicius preserved the orthodox Neoplatonic doctrine (Ammonius and his master Proclus always held to the eternity of the world), whereas the Christian Philoponus opposed this view.

It is astonishing that the grammarian Philoponus (he called himself John the Grammarian and edited most of Ammonius’s lectures on Aristotle’s writings) argued without Christian presuppositions and personal disparagement; Simplicius, however, usually a very modest and well­educated philosopher, very rudely called Philoponus’s arguments “rubbish” and accused him of “bragging and contentiousness.”

Justinian

Justinian

Obviously, they had never met personally (most probably, Simplicius had been working in Athens long before 529 CE, when the academy was closed by Justinian; Philoponus apparently never left Alexandria).

Philoponus argued against the eternity of the world in his commentaries on Aristotle’s Physics (probably written in 517 CE) and Meteorology, then in On the Eternity of the World, Against Proclus (De aeternitate mundi contra Proclum, written in 529 CE; this treatise refutes 18 arguments from a lost treatise written by Proclus about the eternity of the world). The writing Against Aristotle (Contra Aristotelem), which can be dated between approximately 530 CE and 534 CE, is preserved only in fragments.

The first five books contained Philoponus’s criticism of Aristotle’s theory of the fifth element, the sixth book his criticism of Aristotle’s theory of eternal movement, and at least two further books contained reflections about a Christian theory of divine creation. Simplicius’s answer to Philoponus can be found mainly in his commentary on Aristotle’s De caelo I and Physics VIII.

The eternity

The eternity

Philoponus attacks the eternity of the world by demonstrating inner contradictions in Aristotle’s theory of time and eternity and by refuting Aristotle through Aristotle himself.

One argument goes as follows: The eternity of the world is incompatible with Aristotle’s definition of movement, because movement is the act of what is movable in potency, that is, the movable in potency exists prior to the movement.

This implies that the eternal movements (e.g., the heavens’ circular movements) have some movable in potency prior to them (e.g., the heavens), if the movable in potency is always anterior to the movement. Philoponus concludes that the Aristotelian definition of movement is not universal.

finite movement

finite movement

Simplicius defends the universality of Aristotle’s definition of movement by making a difference between infinite and finite movement: In the case of finite movement, the movable is still there, if the movement has finished; in the case of infinite, eternal movement, only one state of movement is prior to another state. For instance, if the sun is in Aries, then it is the movable, which is potentially in Taurus.

Further, if any first movement is excluded, Philoponus argues that all present movements become unintelligible, because every movement presupposes an infinite number of previous movements; we could not avoid a regressus in infinitum.

Moreover, all present movements are added to those of the past; that leads to the evidently absurd notion of an infinite constantly increasing. The same problem arises concerning the future: If time and movement infinitely continue in the future, there would be an infinite body with infinite power.

merely potential

merely potential

But that is not possible, so the world could not exist indefinitely in the future. The core of this argument is Philoponus’s attack on Aristotle’s notion of infinity: Aristotle contends that infinity is merely potential and never actual.

For if you divide a line or a duration, you can actually mark off only a finite number of divisions, either physically or mentally. There is only a potential infinity of divisions, inasmuch as infinity exists through a process of dividing one point (or one now) after another; it is the same with the infinity of numbers.

Philoponus attacks this notion of infinity by several arguments. First, the universe must have had a beginning, or it would by now have traversed an actual infinity of years. The second argument is this: If you suppose an actual infinite number of years up to this year, next year will be an infinity plus one year.

fundamental difference

fundamental difference

So the infinity is increasing. Simplicius says Aristotle had already anticipated Philoponus’s objections, for he had pointed out that the past years have finished, so you do not get an actual infinity of them existing.

That implies that time and movement are not an actually infinite quantity, but their infinity means there is a possibility of transcending every given limitation. The most fundamental difference between Philoponus and Simplicius is this: Whereas, Simplicius’s infinite time is a circular indefinite repetition of finite times, Philoponus’s notion of time is linear.

However, the rejection of Philoponus’s argument appears difficult in the context of Aristotle’s philosophy of nature if you want to preserve the singularity of the individual parts of time, for instance, days or hours.

Pure Reason

Pure Reason

Philoponus’s arguments against the eternity of the world were repeated by Bonaventure in the 13th century, after the arguments had been elaborated by Islamic philosophers. Finally, the dispute between Philoponus and Simplicius has an equivalent in Kant’s doctrine of the “antinomy of pure reason” in his Critique of Pure Reason, especially the “first conflict of transcendental ideas.”

One branch of the antinomy is equivalent to Philoponus’s argument (in Kant’s words, “The world has a beginning in time”); this and the opposite argu­ ment (“the world has no beginning in time”) is equivalent to Simplicius.

Probably, there is not any “immediate effective historical connection” between the Alexandrian school quarrel and Kant’s cosmological antinomy, but it shows that in this quarrel, “Greek thinking comes to the limits of its own presuppositions.”

Alexandrian school

Alexandrian school

Philosopher’s Stone


philosopher stone

philosopher stone

The philosopher’s stone is a substance, tincture, or item created through alchemy that is supposed to change base metals into more precious ones and has the ability to extend one’s life, cure sickness, and even grant immortality.

Western traditions of alchemy are more closely associated with the concept of the philosopher’s stone; the Eastern traditions of alchemy were more closely associated with the concept of the elixir of life.

Europeans probably discovered Islamic alchemy following the influence brought about by the Crusades. Islamic alchemy has its roots in Alexandria, which combined various traditions of both Greece and Egypt.

the crusades

the crusades

The Western traditions were much more involved with the idea of changing base metals into higher or noble metals (gold or silver from lead) with longevity as a secondary effect. That is not to say that there was no interest in longevity, but that wealth was the primary motivator for many alchemists in Western Europe.

There were some European alchemists, however, who pursued the aspects of longevity as well as those of healing. Paracelsus (1493–1541) was both a physician and alchemist, using alchemy to cure the sick and pursuing the art in a different manner than others before him.

He was one of the first to separate the pursuit of transmuting metals (alchemia transmutatoria) from that of healing (alchemia medica). Paracelsus is also considered the founder of toxicology. He died at the age of 48, possibly of cancer, somewhat young for one devoted to pursuing longevity and healing.

Nicolas Flamel

Nicolas Flamel

Another well­known alchemist associated with the philosopher’s stone is Nicolas Flamel (1330–1418). He began a career as a scrivener but found a small book on alchemy that he wanted to understand and began his career as an alchemist.

Several books are attributed to him and describe his pursuit of the philosopher’s stone, but many scholars now believe that some of these works were written later by others to lend legitimacy to the field of alchemy and the pursuit of longevity.

There are myths surrounding the death of Flamel and his wife; notably, the legend that he did not die but faked his death and is still living today on his discovery of the philosopher’s stone. Again, these legends are attributed to those who want to add to the legitimacy of the field of alchemy.

Eastern tradition

Eastern tradition

As with the Eastern tradition of alchemy, the Western tradition became more and more philosophical or transcendental. The idea that the transmutation of a human was less a physical process and more of a spiritual exercise, and not achievable through any physical process, became important as the role of science became more prevalent.

Scientists continued to make discoveries regarding the immutability of metals and, by extension, humans also could not physically transmute. Therefore, they had to do so internally, through mysticism, philosophy, or some other transcendental means.

In one respect, Nicolas Flamel and others have achieved a kind of immortality. As seen in some of today’s popular media (e.g., the Harry Potter movies, and the Da Vinci Code novel by Dan Brown), Flamel has lived on, although not in the way he intended.

Dan Brown

Dan Brown

Phi Phenomenon


phi phenomenon

phi phenomenon

The phi phenomenon is a type of apparent move­ment or an illusion of movement. It is also known as stroboscopic movement. In fact the phi phe­nomenon consists of three types of apparent movement: beta, gamma, and delta movements.

For reasons of space, we shall elaborate only on the first, the beta movement. As in the case of the tau and kappa illusions, the phi phenomenon illustrates the complex nature of the interrelations between the perceptions of movement, distance, and time.

The apparent movement occurs when two physically distinct stimuli—say, two light points— are alternately displayed at a frequency that exceeds a certain threshold value. Under such con­ditions, a continuous movement from one stimulus to the other is perceived.

relevant sensory

relevant sensory

The apparent movement’s characteristics depend on a number of factors: the physical spatial distance between the two stimuli; the physical intensity of the stimuli, which deter­ mines the amount of energy reaching the relevant sensory apparatus in the perceiver; and the dura­tion or time span between appearance of one stimulus and the next.

If the distance and intensity factors are kept constant, then when the time span between the first stimulus and the second is approximately 20 milliseconds, this will result in a perceptual experience of simultaneity.

When the time span is increased to approximately 60 milli­seconds, this will result in a perception of continu­ ous movement between the two stimuli. At approximately 200 milliseconds, the resulting perception will be of one stimulus followed by the next, without any movement between them.

apparent movement

apparent movement

By 1915, the psychologist A. Korte had defined the conditions for apparent movement as follows:

  • If the intensity of stimuli is kept constant, then the time span needed for optimal apparent movement changes in direct proportion to the changes in distance between the stimuli.
  • If the time span between stimuli is kept constant, then the required distance between them in order to generate optimal apparent movement changes in direct proportion to stimuli intensity.
  • If the distance between stimuli is kept constant, then the stimulus intensity required for optimal apparent movement is inversely proportionate to the time span between the first stimulus and the second one.

Some researchers, however, have questioned the relevance of light intensity—in the visual case—for apparent movement.

Beta movement is a continuous apparent move­ment between two, closely adjacent static light points that alternate lighting up. Continuous movement is perceived when the frequency at which the lights go on and off exceeds a certain threshold value, which depends on the distance between the two light points.

significant factor

significant factor

Some researchers believe that light intensity is a significant factor here as well. Beta movement is used, for instance, on billboards that are actually made up out of tiny static light points: Each couple of adjacent light points switches on and off at an appropriate frequency and thus the flowing effect we are all familiar with is created.

Cinema is the ultimate application of the beta phenomenon. The audience is presented with projections of static images at a frequency that ranges between 12 and 24 images per second, and this is what creates the experience of con­tinuous movement.

Another manifestation of beta movement is its tactile variant: This occurs when an apparent sense of movement is experienced between two adjacent locations on the skin when they receive alternating stimulations.

time span

time span

Here, too, the felt quality of the resulting apparent movement will depend on fac­tors of distance between the two locations, the time span between one stimulus and the next, and—according to some researchers—on stimulus intensity.

The existence of the tactile phenomenon indicates that the phi phenomenon is a fundamen­tal physical principle that is not specific to one sensory modality.

The first to describe the phi phenomenon was Max Wertheimer (1912), a Gestalt psychologist. The phenomenon served as early empirical evidence for Gestaltist psychologists’ claim that perceptual experience cannot be explained by means of a one­ to­one relation between proximal stimulus and sensory process.

Max Wertheimer

Max Wertheimer

There is no fit, in the case of the phi phenomenon, between the perceived movement and the external physical stimuli, which are actually static. In the visual case, even though there is no motion of a retinal image, there is a perceptual experience of movement.

And so, the basic argument of the Gestaltists is that a perceptual experi­ence does not constitute a simple mapping of the external stimulus. Perceptual processes, in fact, reflect rules of perceptual organization that the per­ceptual system imposes on the external stimulus.

The phi phenomenon has not been fully and exactly explained to date. Explanations relating to the visual variant refer to the persistence of vision and to the existence of a degree of temporal overlap in the activity of adjacent receptors on the retina.

reti­nal image

reti­nal image

Persistence of vision occurs as a retinal image continues to exist for one sixteenth of a second after the disappearance of an external stimulus. Hence, if a second stimulus occurs, creating a reti­nal image on an adjacent receptor within that time span (i.e., within less than one sixteenth of a sec­ond), what emerges is a temporal overlap between the activities of the two receptors. This then leads to the emergence of the perception of apparent movement.

Time-lapse Photography


Time-lapse Photography

Time-lapse Photography

The purpose of using time­-lapse photography is to speed up events that normally take considerable time. A simple example is the opening of a flower. In a sense, it is just the opposite of the process used in creating slow ­motion pictures. Both processes involve a technique for intentionally altering a normal duration of time in order to learn more about the subject by closer examination.

But, whereas slow­-motion focuses only on the specific subject being filmed at the time, time-lapse photography can record processes that in real time take or months or years to be completed. With both techniques, humans are able to effectively manipulate time for their own practical or artistic purposes.

In time­-lapse photography, the photographer takes a sequence of pictures at a slower rate than the standard 24 frames per second used by the movie industry. The special skills needed to perform time-­lapse photography include being able to discern how much time should be allowed to lapse between each photograph being taken, so as to record discernable changes that are occurring.

movie industry

movie industry

Time intervals may need to be adjusted depending on the particular changes the subject is undergoing, but the process will usually involve taking individual pictures over 24­hour periods for as long as is needed to record the entire process. The effects of both temperature and light must also always be considered.

John Ott is generally considered a pioneer in time­lapse photography. What began as a hobby in his high school days in the late 1920s developed into a career in which his skills became influential.

Because this type of photography was relatively unexplored, he had to use whatever equipment was available and to devise improved equipment himself until he was satisfied that he was photographing subjects in their most realistic setting.

high school

high school

Starting with a Brownie camera and a timer made from kitchen clock works, he eventually built an automatic plastic greenhouse. He developed the ability to take microscopic pictures, as well as a process known as “total spectrum lighting.”

Ott witnessed growing interest in uses of timelapse photography beyond entertainment and advertising, such as applications in horticulture and medicine. He received numerous honors, including an honorary degree from Loyola University, and eventually became a faculty member in the Department of Horticulture at Michigan State University. He worked as a researcher for various companies, including Quaker Oats and General Electric.

In working with Walt Disney on the film Secrets of Life, which was to include a segment on the growth of an apple, Ott discovered that ordinary glass would not transmit all the ultraviolet and shorter wavelengths needed to accurately record the normal process. He was finally able to complete the assignment by substituting special plastic materials.

Walt Disney

Walt Disney

In his film Our Changing World, he wanted to depict the orderly progressions of earth and the creation of life and its development. The power of the single cell had always impressed him. He noted that humankind has been on earth a much shorter time than plants and that plants and animals tend to respond similarly to light.

Though Ott had said that his work was often slow and discouraging, his pioneering efforts were very impressive. His advances encouraged others to devise and use more sophisticated techniques and equipment. Those working with the process continued to emphasize the importance of correct lighting and determining the most appropriate time intervals between pictures.

Time­lapse photography has been used in many scientific studies, such as research on glacier motion in Glacier National Park, studies of sleep patterns, studies of slow­acting geologic processes in natural settings, studies of movement in plants, and studies of weather phenomena.

Glacier National Park

Glacier National Park

In addition to exploring the natural world, there are also many other potential applications of time­lapse photography with respect to human activities, such as monitoring business projects and procedures, and studying the urban environment and urban renewal.

An example of a successful project related to the urban landscape can be found in the work of Camilio Jose Vergara, a photographer, sociologist, and ethnographer. For 30 years he recorded the changes in inner­city neighborhoods in New York, Newark, Chicago, Detroit, and Los Angeles.

Perhaps one of the most dramatic uses has occurred at Ground Zero, the site of the World Trade Center disaster. Documentary filmmaker Jim Whitaker initiated Project Rebirth in the spring of 2002, with the goal of recording what was happening in this area. As the project continued, cameras were installed at all four corners and at ground level.

Ground Zero

Ground Zero

Some results of the ongoing process are available on the Project Rebirth Web site. The process involves taking one frame every 5 minutes for 7 days a week; the final result will be viewable within a span of 20 minutes.

Photosynthesis


Photosynthesis

Photosynthesis

Photosynthesis is the process by which organisms convert light energy into chemical energy in the form of carbohydrates. The inputs of the chemical reaction are light energy, carbon dioxide, and water; the outputs are carbohydrates and oxygen. The overall reaction, which has many intermediate steps, is written as follows:

Light energy + CO2 + H2O => (CH2O) + O2

The sun is the main source of light for the process. Photosynthetic organisms break down the bonds in the resulting carbohydrates to obtain the necessary energy for life­sustaining functions.

Plants, algae, and some bacteria are the known organisms capable of photosynthetic activity. They all produce pigments, specialized proteins that capture energy when exposed to light.

photosynthetic activity

photosynthetic activity

Numerous photosynthetic organisms have developed adaptations to regulate the timing of photosynthesis. By lengthening the time spent in photosynthesis per day or changing the time of day when photosynthesis occurs, organisms improve the efficiency of photosynthesis and their ability to survive.

Locations and Functions of Pigments

The location of pigments in photosynthetic organisms depends on whether the organism is prokaryotic (does not have a cell nucleus or organelles) or eukaryotic (has cell nucleus and organelles). The prokaryote Halobacterium halobium and other photosynthetic bacteria have pigments embedded in their cell membranes.

Prokaryotic blue­green alga has pigment proteins inserted in a more complicated system of stacked membranes interior to the cell wall. Higher plants, such as needle­leaved plants and flowering plants, have a specialized organelle for photosynthesis within the plant cell, the chloroplast. The double­ membraned organelle contains photosynthetic membranes that are embedded most commonly with the pigments, chlorophyll­-a and chlorophyll­-b.

Locations and Functions of Pigments

Locations and Functions of Pigments

Pigments are essential to photosynthesis, because they can absorb energy from photons, the units of light energy. Each pigment absorbs a characteristic wavelength, which is a stream of photons. For example, chlorophyll­a absorbs wavelengths in the range between 550 and 700 nanometers (nm, 1 x 10–9 meter), and bacteriochlorophyll­a in bacteria absorbs wavelengths between 470 and 750 nanometers.

Pigments efficiently absorb energy because they contain chemical bonds that accommodate fluctuating levels of energy. The characteristic carbon rings in pigments include many double bonds.

Carbon atoms joined by double bonds share their electrons; thus the electrons are not strongly attracted to a particular carbon nucleus and move in a loose cloud around the entire molecule. When photons strike a pigment, their energy is accepted by the pigment’s electrons, which can easily move from a lower energy level to a higher one in the cloud of electrons.

energized electrons

energized electrons

Chlorophyll­a has five carbon rings with a total of 10 double bonds, making it an excellent acceptor of energy from light. The pigment can either donate the energized electrons to other molecules or release the energy from the electrons as longer wavelengths than those the pigment absorbed.

Structures in Photosynthesis

Organisms have structures in their photosynthetic membranes called reaction centers and antennae, respectively, both of which are necessary for photosynthesis to occur.

The reaction center is composed of the unique pigments capable of initiating the chemical reactions of photosynthesis by donating electrons to molecules within cells; the pigments are bacteriochlorophyll­a in bacteria and chlorophyll­a in algae and plants. Scientists have identified special forms of these chlorophylls that are responsible for the actual work of changing light energy into chemical energy in the reaction centers.

Structures in Photosynthesis

Structures in Photosynthesis

The chlorophylls are P870 in bacteria and P700 and P680 in algae and plants, where P stands for pigment and the number refers to an absorption wavelength. However, the specialized chlorophylls cannot absorb enough light energy on their own to drive photosynthesis; they are fed energy by the antennae.

The antenna structure in membranes is the locus of light energy absorption and concentration. It is composed of accessory pigments that generally can absorb shorter wavelengths than P680, P700, and P870 can. Examples of accessory pigments are bacteriochlorophyll­b (absorbs 400 nm–1020 nm wavelengths) in purple bacteria and chlorophyll­b (absorbs 454 nm–670 nm wavelengths) in higher plants.

Accessory pigments capture light energy and then release it to other accessory pigments or chlorophylls in the antennae as longer wavelengths, but these accessory pigments are not capable of donating electrons to other molecules. The accessory pigments pass along longer wavelengths to each other until the waves reach a length that can be absorbed by the specialized chlorophylls in the reaction center.

pigment proteins

pigment proteins

A substantial number of accessory pigment proteins are needed to feed a reaction center with enough light energy to drive photosynthesis. Over 300 molecules of chlorophyll­b are needed to funnel enough light energy to activate one molecule of chlorophyll­a in the reaction center of a typical higher plant.

Adaptations in Photosynthesis

Photosynthetic organisms are capable of making photosynthesis more efficient by regulating the time spent in photosynthesis per day or changing the time of day when photosynthesis occurs. Some higher plants can change their leaf position over the course of a day to track the sun’s movement.

This adaptation allows the plants to increase the number of hours per day spent in direct sunlight and maximum light absorption. Experiments have confirmed that this behavior, called diaheliotropism, increases the efficiency of photosynthesis.

Adaptations in Photosynthesis

Adaptations in Photosynthesis

Plants that live in hot, dry climates, such as cacti, have developed an adaptation of photosynthesis that allows parts of the process to occur at a different time of day than in the majority of plants.

Generally, all steps of photosynthesis occur during daylight, including the intake of carbon dioxide through stomata, which are openings in the leaves of plants. The majority of plants take in carbon dioxide and initially fix the carbon into a compound called 3­phosphoglycerate.

However, plants in hot, arid regions lose water at a high rate when the stomata are open, so many have developed crassulacean acid metabolism (CAM) to avoid dehydration. CAM plants open their stomata only at night, initially fix carbon dioxide into malic acid, and then store the acid.

carbon dioxide

carbon dioxide

During the day, CAM plants close their stomata, break down the malic acid to release the carbon dioxide, and then proceed with photosynthesis. The CAM adaptation makes it possible for plants to withstand long periods of drought.

Phylogeny


phylogeny

phylogeny

A phylogeny is an evolutionary history of an organism or group of organisms; it may be interpreted as a genealogical tree, an ancestor and descendant lineage, or as systematic relationships of form within a classification scheme. Phylogenies are studied principally in the fields of phylogenetics and systematics.

History of Phylogenetics

Phylogeny was discussed in detail by the 19th-­century German morphologist Ernst Haeckel, who proposed a biogenetic law (or the law of recapitulation). The biogenetic law states that phylogeny, or the evolutionary history of an organism, is recapitulated through its ontogeny, or the development of an individual organism in embryo.

The subsequent rejection of Haeckel’s law was a significant move away from using mechanical explanations or causes, such as embryonic development, to explain the relationship between organisms. Haeckel’s most significant contribution was that of the phylogenetic tree (Phylogenetisches Stambaum), the now universally accepted way to depict genealogical relationships.

History of Phylogenetics

History of Phylogenetics

A phylogenetic tree may depict hypothetical ancestor­descendant relationships, sometimes called a transformation series, between groups of organisms (species, genera, and families) or their characteristics, through time. Such phylogenetic trees have been popular tools of paleontologists who use them to establish so­called ghost lineages between similar­looking fossils throughout the stratigraphic record.

Phylogenetic trees were challenged in the early 20th century by the German­speaking systematic morphologists, led by Adolf Naef. The evolutionary relationships that phylogenetic trees were claimed to depict were based on linking similar­looking organisms that overlapped through time, rather than considering relationships of form.

The systematic morphologists considered homologues (different manifestations of the same morphological structure) to be a sounder basis for the discovery of relationship than the assembly of ghost lineages. If organisms are related, their characters are homologous, that is, the same; as opposed to analogous, that is, similar but not the same.

hypothetical lineages

hypothetical lineages

Naef’s trees related organisms only at the terminal branches, rather than depicting hypothetical lineages, with organisms (hypothetical or real) at both the nodes and tips. Homologous organisms belonged to “natural groups or classifications” that share a greater relationship among themselves than they do to any other group.

The rejection of phylogenetic trees and the concomitant support for natural groups was criticized by Anglo American phylogeneticists such as George Gaylord Simpson and Ernst Mayr, who defended the depiction of lineages in phylogenetic trees rather than the discovery of natural groups, which challenged some traditional taxonomic groups.

Anglo American phylogenetics, however, changed considerably in the latter half of the 20th century when the work of Willi Hennig, a German entomologist, was translated into English.

Phylogenetic Systematics

Phylogenetic Systematics

Phylogenetic Systematics

Hennig’s Phylogenetic Systematics attempted to resurrect Haeckel’s systematic phylogenetics by reintroducing the causal mechanisms that had been rejected by Adolf Naef.

Hennig’s phylogenetic systematics combined Haeckel’s transformational viewpoint—but at the level of character rather than taxon—with Naef’s trees of relationships to form ancestor­descendant schemes of relationship with organisms only at the tips, and character transformations leading from the nodes to the tips.

The resulting trees attempted to group homologous organisms into “natural” or monophyletic classifications based on a causal mechanism, thus combining Haeckel’s phylogenetic tree with Naef’s systematic morphology.

numerical method

numerical method

Phylogenetic systematics developed into a numerical method by incorporating the principal notion of phenetics, that is, similarity concepts, with a causal mechanism to find optimal trees.

Phylogenetic systematics, later referred to as cladistics, underwent a revolution in the work of Gareth Nelson by returning to systematic morphology. Pattern cladistics rejected causal homologies and ancestor­descendant relationships as uninformative and misleading, because they introduced bias into phylogenetics.

The pattern cladists, led by Ronald Brady and Gareth Nelson, considered monophyly to indicate “natural groups,” which can be used to test existing taxonomies rather than to identify causal relationships (a common ancestor). The resulting diagrams, called cladograms, could represent numerous lineages but only a single classification.

Colin Patterson

Colin Patterson

Hennig’s elimination of paraphyly and its connection made with ancestry by cladists such as Colin Patterson helped to define phylogenetics as a science of classification based on the relationships of form.

Molecular Phylogenetics

Molecular phylogenetics is the study of amino acid or DNA sequences and how they may be related among different organisms. The field has grown exponentially and amassed a significant volume of data.

Unlike phylogenetic systematics, molecular phylogenies tend to consist of individual character trees (relationships between organisms based on a single character) and are used to hypothesize recent genealogies in populations as well as ancestor­descendant relationships in species.

DNA sequences

DNA sequences

Despite its popularity, very little theoretical work has been done on the relevance of homology of DNA sequences. Molecular phylogenetics, however, has progressed methodologically and technologically in such issues as alignment of sequences and in mapping the similarity distances in phenetic methods.

Phylogenetic Classification

Phylogenies may be interpreted as explicit evolutionary pathways, natural groups (classifications), or a combination of both. The latter has caused the most controversy in its claim for phylogenetic classifications.

Recent debate has focused on defend­ ing lineages rather than classifications in taxonomy. A nonmonophyletic group (also known as a paraphyletic or polyphyletic group) is an artificial or incongruous set that shares greater relationship to other groups than to its own.

Phylogenetic Classification

Phylogenetic Classification

A proposed lineage may be paraphyletic and therefore contradict any given natural classification. Reptiles are an example of a paraphyletic group that exists in name only, not within a natural classification.

The defense of paraphyletic groups in classification reflects the battle between the Anglo American paleontologists and systematic morphologists in the early 20th century, during which classification and hypothetical lineages were confused.

Phylogenetic Biogeography

Phylogenies have been used in biogeography (the study of biotic distributions) during three periods: in the late 19th century, with the advent of natural selection as a viable mechanism for species evolution (e.g., Haeckel); in the 1960s, with the onset of Hennig’s phylogenetic systematics; and in the late 20th century, with the use of molecular phylogenies.

Phylogenetic Biogeography

Phylogenetic Biogeography

The same method has been used in each of these periods, namely that of proposing a center of origin and drawing the direction of dispersal and/or vicariance events (allopatry) on a phylogenetic tree.

Since the late 19th century, fossils were used to date such events within any given phylogenetic tree. The method is still widely practiced today (i.e., using a molecular clock). The only difference between these periods is the data used.

Nineteenth­-century phylogeneticists relied on fossils, mid­-20th-­century phylogeneticists on the morphology of extant taxa, and 21st-­century molecular systematists on molecular data.

molecular systematists

molecular systematists