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Saturday, March 6, 2021

Origin of avian flight

From Wikipedia, the free encyclopedia
 
The Berlin Archaeopteryx, one of the earliest known birds.

Around 350 BCE, Aristotle and other philosophers of the time attempted to explain the aerodynamics of avian flight. Even after the discovery of the ancestral bird Archaeopteryx over 150 years ago, debates still persist regarding the evolution of flight. There are three leading hypotheses pertaining to avian flight: Pouncing Proavis model, Cursorial model, and Arboreal model.

In March 2018, scientists reported that Archaeopteryx was likely capable of flight, but in a manner substantially different from that of modern birds.

Flight characteristics

For flight to occur in Aves, four physical forces (thrust and drag, lift and weight) must be favorably combined. In order for birds to balance these forces, certain physical characteristics are required. Asymmetrical wings, found on all flying birds with the exception of hummingbirds, help in the production of thrust and lift. Anything that moves through the air produces drag due to friction. The aerodynamic body of a bird can reduce drag, but when stopping or slowing down a bird will use its tail and feet to increase drag. Weight is the largest obstacle birds must overcome in order to fly. An animal can more easily attain flight by reducing its absolute weight. Birds evolved from other theropod dinosaurs that had already gone through a phase of size reduction during the Middle Jurassic, combined with rapid evolutionary changes. Flying birds during their evolution further reduced relative weight through several characteristics such as the loss of teeth, shrinkage of the gonads out of mating season, and fusion of bones. Teeth were replaced by a lightweight bill made of keratin, the food being processed by the bird's gizzard. Other advanced physical characteristics evolved for flight are a keel for the attachment of flight muscles and an enlarged cerebellum for fine motor coordination. These were gradual changes, though, and not strict conditions for flight: the first birds had teeth, at best a small keel and relatively unfused bones. Pneumatic bone, that is hollow or filled with air sacs, has often been seen as an adaptation reducing weight, but it was already present in non-flying dinosaurs, and birds on average do not have a lighter skeleton than mammals of the same size. The same is true for the furcula, a bone which enhances skeletal bracing for the stresses of flight.

The mechanics of an avian's wings involve a complex interworking of forces, particularly at the shoulder where most of the wings' motions take place. These functions depend on a precise balance of forces from the muscles, ligaments, and articular cartilages as well as inertial, gravitational, and aerodynamic loads on the wing.

Birds have two main muscles in their wing that are responsible for flight: the pectoralis and the supracoracoideus. The pectoralis is the largest muscle in the wing and is the primary depressor and pronator of the wing. The supracoracoideus is the second largest and is the primary elevator and supinator. In addition, there are distal wing muscles that assist the bird in flight.

Prior to their existence on birds, feathers were present on the bodies of many dinosaur species. Through natural selection, feathers became more common among the animals as their wings developed over the course of tens of millions of years. The smooth surface of feathers on a bird's body helps to reduce friction while in flight. The tail, also consisting of feathers, helps the bird to maneuver and glide.

Hypotheses

Pouncing Proavis model

A theory of a pouncing proavis was first proposed by Garner, Taylor, and Thomas in 1999:

We propose that birds evolved from predators that specialized in ambush from elevated sites, using their raptorial hindlimbs in a leaping attack. Drag–based, and later lift-based, mechanisms evolved under selection for improved control of body position and locomotion during the aerial part of the attack. Selection for enhanced lift-based control led to improved lift coefficients, incidentally turning a pounce into a swoop as lift production increased. Selection for greater swooping range would finally lead to the origin of true flight.

The authors believed that this theory had four main virtues:

  • It predicts the observed sequence of character acquisition in avian evolution.
  • It predicts an Archaeopteryx-like animal, with a skeleton more or less identical to terrestrial theropods, with few adaptations to flapping, but very advanced aerodynamic asymmetrical feathers.
  • It explains that primitive pouncers (perhaps like Microraptor) could coexist with more advanced fliers (like Confuciusornis or Sapeornis) since they did not compete for flying niches.
  • It explains that the evolution of elongated rachis-bearing feathers began with simple forms that produced a benefit by increasing drag. Later, more refined feather shapes could begin to also provide lift.

Cursorial model

A cursorial, or "running" model was originally proposed by Samuel Wendell Williston in 1879. This theory states that "flight evolved in running bipeds through a series of short jumps". As the length of the jumps extended, the wings were used not only for thrust but also for stability, and eventually eliminated the gliding intermediate. This theory was modified in the 1970s by John Ostrom to describe the use of wings as an insect-foraging mechanism which then evolved into a wing stroke. Research was conducted by comparing the amount of energy expended by each hunting method with the amount of food gathered. The potential hunting volume doubles by running and jumping. To gather the same volume of food, Archaeopteryx would expend less energy by running and jumping than by running alone. Therefore, the cost/benefit ratio would be more favorable for this model. Due to Archaeopteryx's long and erect leg, supporters of this model say the species was a terrestrial bird. This characteristic allows for more strength and stability in the hindlimbs. Thrust produced by the wings coupled with propulsion in the legs generates the minimum velocity required to achieve flight. This wing motion is thought to have evolved from asymmetrical propulsion flapping motion. Thus, through these mechanisms, Archaeopteryx was able to achieve flight from the ground up.

Although the evidence in favor of this model is scientifically plausible, the evidence against it is substantial. For instance, a cursorial flight model would be energetically less favorable when compared to the alternative hypotheses. In order to achieve liftoff, Archaeopteryx would have to run faster than modern birds by a factor of three, due to its weight. Furthermore, the mass of Archaeopteryx versus the distance needed for minimum velocity to obtain liftoff speed is proportional, therefore, as mass increases, the energy required for takeoff increases. Other research has shown that the physics involved in cursorial flight would not make this a likely answer to the origin of avian flight. Once flight speed is obtained and Archaeopteryx is in the air, drag would cause the velocity to instantaneously decrease; balance could not be maintained due to this immediate reduction in velocity. Hence, Archaeopteryx would have a very short and ineffective flight. In contrast to Ostrom's theory regarding flight as a hunting mechanism, physics again does not support this model. In order to effectively trap insects with the wings, Archaeopteryx would require a mechanism such as holes in the wings to reduce air resistance. Without this mechanism, the cost/benefit ratio would not be feasible.

The decrease in efficiency when looking at the cursorial model is caused by the flapping stroke needed to achieve flight. This stroke motion needs both wings to move in a symmetrical motion, or together. This is opposed to an asymmetrical motion like that in humans' arms while running. The symmetrical motion would be costly in the cursorial model because it would be difficult while running on the ground, compared to the arboreal model where it is natural for an animal to move both arms together when falling. There is also a large fitness reduction between the two extremes of asymmetrical and symmetrical flapping motion so the theropods would have evolved to one of the extremes. However, new research on the mechanics of bipedal running has suggested that oscillations produced by the running motion could induce symmetrical flapping of the wings at the natural frequency of the oscillation.

Wing-assisted incline running

The WAIR hypothesis, a version of the "cursorial model" of the evolution of avian flight, in which birds' wings originated from forelimb modifications that provided downforce, enabling the proto-birds to run up extremely steep slopes such as the trunks of trees, was prompted by observation of young chukar chicks, and proposes that wings developed their aerodynamic functions as a result of the need to run quickly up very steep slopes such as tree trunks, for example to escape from predators. Note that in this scenario birds need downforce to give their feet increased grip. It has been argued that early birds, including Archaeopteryx, lacked the shoulder mechanism by which modern birds' wings produce swift, powerful upstrokes; since the downforce on which WAIR depends is generated by upstrokes, it seems that early birds were incapable of WAIR. However, a study that found lift generated from wings to be the primary factor for successfully accelerating a body toward a substrate during WAIR indicated the onset of flight ability was constrained by neuromuscular control or power output rather than by external wing morphology itself and that partially developed wings not yet capable of flight could indeed provide useful lift during WAIR. Additionally, examination of the work and power requirements for extant bird pectoralis contractile behavior during WAIR at different angles of substrate incline demonstrated incremental increases in these requirements, both as WAIR angles increased and in the transition from WAIR to flapping flight. This provides a model for an evolutionary transition from terrestrial to aerial locomotion as transitional forms incrementally adapted to meet the work and power requirements to scale steeper and steeper inclines using WAIR and the incremental increases from WAIR to flight.

Birds use wing-assisted inclined running from the day they hatch to increase locomotion. This can also be said for birds or feathered theropods whose wing muscles cannot generate enough force to fly, and shows how this behavior could have evolved to help these theropods then eventually led to flight. The progression from wing-assisted incline running to flight can be seen in the growth of birds, from when they are hatchlings to fully grown. They begin with wing-assisted incline running and slowly alter their wing strokes for flight as they grow and are able to make enough force. These transitional stages that lead to flight are both physical and behavioral. The transitions over a hatchling's life can be correlated with the evolution of flight on a macro scale. If protobirds are compared to hatchlings their physical traits such as wing size and behavior may have been similar. Flapping flight is limited by the size and muscle force of a wing. Even while using the correct model of arboreal or cursorial, protobirds' wings were not able to sustain flight, but they did most likely gain the behaviors needed for the arboreal or cursorial model like today's birds do when hatched. There are similar steps between the two. Wing-assisted incline running can also produce a useful lift in babies but is very small compared to that of juveniles and adult birds. This lift was found responsible for body acceleration when going up an incline and leads to flight as the bird grows.

Arboreal model

This model was originally proposed in 1880 by Othniel C. Marsh. The theory states Archaeopteryx was a reptilian bird that soared from tree to tree. After the leap, Archaeopteryx would then use its wings as a balancing mechanism. According to this model, Archaeopteryx developed a gliding method to conserve energy. Even though an arboreal Archaeopteryx exerts energy climbing the tree, it is able to achieve higher velocities and cover greater distances during the gliding phase, which conserves more energy in the long run than a cursorial bipedal runner. Conserving energy during the gliding phase makes this a more energy-efficient model. Therefore, the benefits gained by gliding outweigh the energy used in climbing the tree. A modern behavior model to compare against would be that of the flying squirrel. In addition to energy conservation, arboreality is generally associated positively with survival, at least in mammals.

The evolutionary path between arboreality and flight has been proposed through a number of hypotheses. Dudley and Yanoviak proposed that animals that live in trees generally end up high enough that a fall, purposeful or otherwise, would generate enough speed for aerodynamic forces to have an effect on the body. Many animals, even those which do not fly, demonstrate the ability to right themselves and face the ground ventrally, then exhibiting behaviors that act against aerodynamic forces to slow their rate of descent in a process known as parachuting. Arboreal animals that were forced by predators or simply fell from trees that exhibited these kinds of behaviors would have been in a better position to eventually evolve capabilities that were more akin to flight as we know them today.

Researchers in support of this model have suggested that Archaeopteryx possessed skeletal features similar to those of modern birds. The first such feature to be noted was the supposed similarity between the foot of Archaeopteryx and that of modern perching birds. The hallux, or modified of the first digit of the foot, was long thought to have pointed posterior to the remaining digits, as in perching birds. Therefore, researchers once concluded that Archaeopteryx used the hallux as a balancing mechanism on tree limbs. However, study of the Thermopolis specimen of Archeopteryx, which has the most complete foot of any known, showed that the hallux was not in fact reversed, limiting the creature's ability to perch on branches and implying a terrestrial or trunk-climbing lifestyle. Another skeletal feature that is similar in Archaeopteryx and modern birds is the curvature of the claws. Archaeopteryx possessed the same claw curvature of the foot to that of perching birds. However, the claw curvature of the hand in Archaeopteryx was similar to that in basal birds. Based upon the comparisons of modern birds to Archaeopteryx, perching characteristics were present, signifying an arboreal habitat. The ability for takeoff and flight was originally thought to require a supracoracoideus pulley system (SC). This system consists of a tendon joining the humerus and coracoid bones, allowing rotation of the humerus during the upstroke. However, this system is lacking in Archaeopteryx. Based on experiments performed by M. Sy in 1936, it was proven that the SC pulley system was not required for flight from an elevated position but was necessary for cursorial takeoff.

Synthesis

Some researchers have suggested that treating arboreal and cursorial hypotheses as mutually exclusive explanations of the origin of bird flight is incorrect. Researchers in support of synthesizing cite studies that show incipient wings have adaptive advantages for a variety of functions, including arboreal parachuting, WAIR, and horizontal flap-leaping. Other research also shows that ancestral avialans were not necessarily exclusively arboreal or cursorial, but rather lived on a spectrum of habitats. The capability for powered flight evolved due to a multitude of selective advantages of incipient wings in navigating a more complex environment than previously thought.

Transitional fossil

From Wikipedia, the free encyclopedia

A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group. This is especially important where the descendant group is sharply differentiated by gross anatomy and mode of living from the ancestral group. These fossils serve as a reminder that taxonomic divisions are human constructs that have been imposed in hindsight on a continuum of variation. Because of the incompleteness of the fossil record, there is usually no way to know exactly how close a transitional fossil is to the point of divergence. Therefore, it cannot be assumed that transitional fossils are direct ancestors of more recent groups, though they are frequently used as models for such ancestors.

In 1859, when Charles Darwin's On the Origin of Species was first published, the fossil record was poorly known. Darwin described the perceived lack of transitional fossils as, "... the most obvious and gravest objection which can be urged against my theory," but explained it by relating it to the extreme imperfection of the geological record. He noted the limited collections available at that time, but described the available information as showing patterns that followed from his theory of descent with modification through natural selection. Indeed, Archaeopteryx was discovered just two years later, in 1861, and represents a classic transitional form between earlier, non-avian dinosaurs and birds. Many more transitional fossils have been discovered since then, and there is now abundant evidence of how all classes of vertebrates are related, including many transitional fossils. Specific examples of class-level transitions are: tetrapods and fish, birds and dinosaurs, and mammals and "mammal-like reptiles".

The term "missing link" has been used extensively in popular writings on human evolution to refer to a perceived gap in the hominid evolutionary record. It is most commonly used to refer to any new transitional fossil finds. Scientists, however, do not use the term, as it refers to a pre-evolutionary view of nature.

Evolutionary and phylogenetic taxonomy

Transitions in phylogenetic nomenclature

Traditional spindle diagram showing the vertebrates classes "budding" off from each other. Transitional fossils typically represent animals from near the branching points.

In evolutionary taxonomy, the prevailing form of taxonomy during much of the 20th century and still used in non-specialist textbooks, taxa based on morphological similarity are often drawn as "bubbles" or "spindles" branching off from each other, forming evolutionary trees. Transitional forms are seen as falling between the various groups in terms of anatomy, having a mixture of characteristics from inside and outside the newly branched clade.

With the establishment of cladistics in the 1990s, relationships commonly came to be expressed in cladograms that illustrate the branching of the evolutionary lineages in stick-like figures. The different so-called "natural" or "monophyletic" groups form nested units, and only these are given phylogenetic names. While in traditional classification tetrapods and fish are seen as two different groups, phylogenetically tetrapods are considered a branch of fish. Thus, with cladistics there is no longer a transition between established groups, and the term "transitional fossils" is a misnomer. Differentiation occurs within groups, represented as branches in the cladogram.

In a cladistic context, transitional organisms can be seen as representing early examples of a branch, where not all of the traits typical of the previously known descendants on that branch have yet evolved. Such early representatives of a group are usually termed "basal taxa" or "sister taxa," depending on whether the fossil organism belongs to the daughter clade or not.

Transitional versus ancestral

A source of confusion is the notion that a transitional form between two different taxonomic groups must be a direct ancestor of one or both groups. The difficulty is exacerbated by the fact that one of the goals of evolutionary taxonomy is to identify taxa that were ancestors of other taxa. However, because evolution is a branching process that produces a complex bush pattern of related species rather than a linear process producing a ladder-like progression, and because of the incompleteness of the fossil record, it is unlikely that any particular form represented in the fossil record is a direct ancestor of any other. Cladistics deemphasizes the concept of one taxonomic group being an ancestor of another, and instead emphasizes the identification of sister taxa that share a more recent common ancestor with one another than they do with other groups. There are a few exceptional cases, such as some marine plankton microfossils, where the fossil record is complete enough to suggest with confidence that certain fossils represent a population that was actually ancestral to a later population of a different species. But, in general, transitional fossils are considered to have features that illustrate the transitional anatomical features of actual common ancestors of different taxa, rather than to be actual ancestors.

Prominent examples

Archaeopteryx

Archaeopteryx is one of the most famous transitional fossils and gives evidence for the evolution of birds from theropod dinosaurs.

Archaeopteryx is a genus of theropod dinosaur closely related to the birds. Since the late 19th century, it has been accepted by palaeontologists, and celebrated in lay reference works, as being the oldest known bird, though a study in 2011 has cast doubt on this assessment, suggesting instead that it is a non-avialan dinosaur closely related to the origin of birds.

It lived in what is now southern Germany in the Late Jurassic period around 150 million years ago, when Europe was an archipelago in a shallow warm tropical sea, much closer to the equator than it is now. Similar in shape to a European magpie, with the largest individuals possibly attaining the size of a raven, Archaeopteryx could grow to about 0.5 metres (1.6 ft) in length. Despite its small size, broad wings, and inferred ability to fly or glide, Archaeopteryx has more in common with other small Mesozoic dinosaurs than it does with modern birds. In particular, it shares the following features with the deinonychosaurs (dromaeosaurs and troodontids): jaws with sharp teeth, three fingers with claws, a long bony tail, hyperextensible second toes ("killing claw"), feathers (which suggest homeothermy), and various skeletal features. These features make Archaeopteryx a clear candidate for a transitional fossil between dinosaurs and birds, making it important in the study both of dinosaurs and of the origin of birds.

The first complete specimen was announced in 1861, and ten more Archaeopteryx fossils have been found since then. Most of the eleven known fossils include impressions of feathers—among the oldest direct evidence of such structures. Moreover, because these feathers take the advanced form of flight feathers, Archaeopteryx fossils are evidence that feathers began to evolve before the Late Jurassic.

Australopithecus afarensis

A. afarensis - walking posture.

The hominid Australopithecus afarensis represents an evolutionary transition between modern bipedal humans and their quadrupedal ape ancestors. A number of traits of the A. afarensis skeleton strongly reflect bipedalism, to the extent that some researchers have suggested that bipedality evolved long before A. afarensis. In overall anatomy, the pelvis is far more human-like than ape-like. The iliac blades are short and wide, the sacrum is wide and positioned directly behind the hip joint, and there is clear evidence of a strong attachment for the knee extensors, implying an upright posture.

While the pelvis is not entirely like that of a human (being markedly wide, or flared, with laterally orientated iliac blades), these features point to a structure radically remodelled to accommodate a significant degree of bipedalism. The femur angles in toward the knee from the hip. This trait allows the foot to fall closer to the midline of the body, and strongly indicates habitual bipedal locomotion. Present-day humans, orangutans and spider monkeys possess this same feature. The feet feature adducted big toes, making it difficult if not impossible to grasp branches with the hindlimbs. Besides locomotion, A. afarensis also had a slightly larger brain than a modern chimpanzee (the closest living relative of humans) and had teeth that were more human than ape-like.

Pakicetids, Ambulocetus

Reconstruction of Pakicetus
 
Skeleton of Ambulocetus natans

The cetaceans (whales, dolphins and porpoises) are marine mammal descendants of land mammals. The pakicetids are an extinct family of hoofed mammals that are the earliest whales, whose closest sister group is Indohyus from the family Raoellidae. They lived in the Early Eocene, around 53 million years ago. Their fossils were first discovered in North Pakistan in 1979, at a river not far from the shores of the former Tethys Sea. Pakicetids could hear under water, using enhanced bone conduction, rather than depending on tympanic membranes like most land mammals. This arrangement does not give directional hearing under water.

Ambulocetus natans, which lived about 49 million years ago, was discovered in Pakistan in 1994. It was probably amphibious, and looked like a crocodile. In the Eocene, ambulocetids inhabited the bays and estuaries of the Tethys Ocean in northern Pakistan. The fossils of ambulocetids are always found in near-shore shallow marine deposits associated with abundant marine plant fossils and littoral molluscs. Although they are found only in marine deposits, their oxygen isotope values indicate that they consumed water with a range of degrees of salinity, some specimens showing no evidence of sea water consumption and others none of fresh water consumption at the time when their teeth were fossilized. It is clear that ambulocetids tolerated a wide range of salt concentrations. Their diet probably included land animals that approached water for drinking, or freshwater aquatic organisms that lived in the river. Hence, ambulocetids represent the transition phase of cetacean ancestors between freshwater and marine habitat.

Tiktaalik

Tiktaalik roseae had spiracles (air holes) above the eyes.
 
Life restoration of Tiktaalik roseae

Tiktaalik is a genus of extinct sarcopterygian (lobe-finned fish) from the Late Devonian period, with many features akin to those of tetrapods (four-legged animals). It is one of several lines of ancient sarcopterygians to develop adaptations to the oxygen-poor shallow water habitats of its time—adaptations that led to the evolution of tetrapods. Well-preserved fossils were found in 2004 on Ellesmere Island in Nunavut, Canada.

Tiktaalik lived approximately 375 million years ago. Paleontologists suggest that it is representative of the transition between non-tetrapod vertebrates such as Panderichthys, known from fossils 380 million years old, and early tetrapods such as Acanthostega and Ichthyostega, known from fossils about 365 million years old. Its mixture of primitive fish and derived tetrapod characteristics led one of its discoverers, Neil Shubin, to characterize Tiktaalik as a "fishapod." Unlike many previous, more fish-like transitional fossils, the "fins" of Tiktaalik have basic wrist bones and simple rays reminiscent of fingers. They may have been weight-bearing. Like all modern tetrapods, it had rib bones, a mobile neck with a separate pectoral girdle, and lungs, though it had the gills, scales, and fins of a fish. However in a 2008 paper by Boisvert at al. it is noted that Panderichthys, due to its more derived distal portion, might be closer to tetrapods than Tiktaalik, which might have independently developed similarities to tetrapods by convergent evolution.

Tetrapod footprints found in Poland and reported in Nature in January 2010 were "securely dated" at 10 million years older than the oldest known elpistostegids (of which Tiktaalik is an example), implying that animals like Tiktaalik, possessing features that evolved around 400 million years ago, were "late-surviving relics rather than direct transitional forms, and they highlight just how little we know of the earliest history of land vertebrates."

Amphistium

Modern flatfish are asymmetrical, with both eyes on the same side of the head.
 
Fossil of Amphistium with one eye at the top-center of the head.

Pleuronectiformes (flatfish) are an order of ray-finned fish. The most obvious characteristic of the modern flatfish is their asymmetry, with both eyes on the same side of the head in the adult fish. In some families the eyes are always on the right side of the body (dextral or right-eyed flatfish) and in others they are always on the left (sinistral or left-eyed flatfish). The primitive spiny turbots include equal numbers of right- and left-eyed individuals, and are generally less asymmetrical than the other families. Other distinguishing features of the order are the presence of protrusible eyes, another adaptation to living on the seabed (benthos), and the extension of the dorsal fin onto the head.

Amphistium is a 50-million-year-old fossil fish identified as an early relative of the flatfish, and as a transitional fossil In Amphistium, the transition from the typical symmetric head of a vertebrate is incomplete, with one eye placed near the top-center of the head. Paleontologists concluded that "the change happened gradually, in a way consistent with evolution via natural selection—not suddenly, as researchers once had little choice but to believe."

Amphistium is among the many fossil fish species known from the Monte Bolca Lagerstätte of Lutetian Italy. Heteronectes is a related, and very similar fossil from slightly earlier strata of France.

Runcaria

The Devonian fossil plant Runcaria resembles a seed but lacks a solid seed coat and means to guide pollen.

A Middle Devonian precursor to seed plants has been identified from Belgium, predating the earliest seed plants by about 20 million years. Runcaria, small and radially symmetrical, is an integumented megasporangium surrounded by a cupule. The megasporangium bears an unopened distal extension protruding above the multilobed integument. It is suspected that the extension was involved in anemophilous pollination. Runcaria sheds new light on the sequence of character acquisition leading to the seed, having all the qualities of seed plants except for a solid seed coat and a system to guide the pollen to the seed.

Fossil record

Not every transitional form appears in the fossil record, because the fossil record is not complete. Organisms are only rarely preserved as fossils in the best of circumstances, and only a fraction of such fossils have been discovered. Paleontologist Donald Prothero noted that this is illustrated by the fact that the number of species known through the fossil record was less than 5% of the number of known living species, suggesting that the number of species known through fossils must be far less than 1% of all the species that have ever lived.

Because of the specialized and rare circumstances required for a biological structure to fossilize, logic dictates that known fossils represent only a small percentage of all life-forms that ever existed—and that each discovery represents only a snapshot of evolution. The transition itself can only be illustrated and corroborated by transitional fossils, which never demonstrate an exact half-way point between clearly divergent forms.

The fossil record is very uneven and, with few exceptions, is heavily slanted toward organisms with hard parts, leaving most groups of soft-bodied organisms with little to no fossil record. The groups considered to have a good fossil record, including a number of transitional fossils between traditional groups, are the vertebrates, the echinoderms, the brachiopods and some groups of arthropods.

History

Post-Darwin

A historic 1904 reconstruction of Archæopteryx
 
Reconstruction of Rhynia

The idea that animal and plant species were not constant, but changed over time, was suggested as far back as the 18th century. Darwin's On the Origin of Species, published in 1859, gave it a firm scientific basis. A weakness of Darwin's work, however, was the lack of palaeontological evidence, as pointed out by Darwin himself. While it is easy to imagine natural selection producing the variation seen within genera and families, the transmutation between the higher categories was harder to imagine. The dramatic find of the London specimen of Archaeopteryx in 1861, only two years after the publication of Darwin's work, offered for the first time a link between the class of the highly derived birds, and that of the more primitive reptiles. In a letter to Darwin, the palaeontologist Hugh Falconer wrote:

Had the Solnhofen quarries been commissioned—by august command—to turn out a strange being à la Darwin—it could not have executed the behest more handsomely—than in the Archaeopteryx.

Thus, transitional fossils like Archaeopteryx came to be seen as not only corroborating Darwin's theory, but as icons of evolution in their own right. For example, the Swedish encyclopedic dictionary Nordisk familjebok of 1904 showed an inaccurate Archaeopteryx reconstruction (see illustration) of the fossil, "ett af de betydelsefullaste paleontologiska fynd, som någonsin gjorts" ("one of the most significant paleontological discoveries ever made").

The rise of plants

Transitional fossils are not only those of animals. With the increasing mapping of the divisions of plants at the beginning of the 20th century, the search began for the ancestor of the vascular plants. In 1917, Robert Kidston and William Henry Lang found the remains of an extremely primitive plant in the Rhynie chert in Aberdeenshire, Scotland, and named it Rhynia.

The Rhynia plant was small and stick-like, with simple dichotomously branching stems without leaves, each tipped by a sporangium. The simple form echoes that of the sporophyte of mosses, and it has been shown that Rhynia had an alternation of generations, with a corresponding gametophyte in the form of crowded tufts of diminutive stems only a few millimetres in height. Rhynia thus falls midway between mosses and early vascular plants like ferns and clubmosses. From a carpet of moss-like gametophytes, the larger Rhynia sporophytes grew much like simple clubmosses, spreading by means of horizontal growing stems growing rhizoids that anchored the plant to the substrate. The unusual mix of moss-like and vascular traits and the extreme structural simplicity of the plant had huge implications for botanical understanding.

Missing links

"Java Man" or Pithecanthropus erectus (now Homo erectus), the original "missing link" found in Java in 1891–92.
 
The human pedigree back to amoeba shown as a reinterpreted chain of being with living and fossil animals. From G. Avery's critique of Ernst Haeckel, 1873.

The idea of all living things being linked through some sort of transmutation process predates Darwin's theory of evolution. Jean-Baptiste Lamarck envisioned that life was generated constantly in the form of the simplest creatures, and strove towards complexity and perfection (i.e. humans) through a progressive series of lower forms. In his view, lower animals were simply newcomers on the evolutionary scene.

After On the Origin of Species, the idea of "lower animals" representing earlier stages in evolution lingered, as demonstrated in Ernst Haeckel's figure of the human pedigree. While the vertebrates were then seen as forming a sort of evolutionary sequence, the various classes were distinct, the undiscovered intermediate forms being called "missing links."

The term was first used in a scientific context by Charles Lyell in the third edition (1851) of his book Elements of Geology in relation to missing parts of the geological column, but it was popularized in its present meaning by its appearance on page xi of his book Geological Evidences of the Antiquity of Man of 1863. By that time, it was generally thought that the end of the last glacial period marked the first appearance of humanity; Lyell drew on new findings in his Antiquity of Man to put the origin of human beings much further back. Lyell wrote that it remained a profound mystery how the huge gulf between man and beast could be bridged. Lyell's vivid writing fired the public imagination, inspiring Jules Verne's Journey to the Center of the Earth (1864) and Louis Figuier's 1867 second edition of La Terre avant le déluge ("Earth before the Flood"), which included dramatic illustrations of savage men and women wearing animal skins and wielding stone axes, in place of the Garden of Eden shown in the 1863 edition.

The search for a fossil showing transitional traits between apes and humans, however, was fruitless until the young Dutch geologist Eugène Dubois found a skullcap, a molar and a femur on the banks of Solo River, Java in 1891. The find combined a low, ape-like skull roof with a brain estimated at around 1000 cc, midway between that of a chimpanzee and an adult human. The single molar was larger than any modern human tooth, but the femur was long and straight, with a knee angle showing that "Java Man" had walked upright. Given the name Pithecanthropus erectus ("erect ape-man"), it became the first in what is now a long list of human evolution fossils. At the time it was hailed by many as the "missing link," helping set the term as primarily used for human fossils, though it is sometimes used for other intermediates, like the dinosaur-bird intermediary Archaeopteryx.

Sudden jumps with apparent gaps in the fossil record have been used as evidence for punctuated equilibrium. Such jumps can be explained either by macromutation or simply by relatively rapid episodes of gradual evolution by natural selection, since a period of say 10,000 years barely registers in the fossil record.

While "missing link" is still a popular term, well-recognized by the public and often used in the popular media, the term is avoided in scientific publications. Some bloggers have called it "inappropriate"; both because the links are no longer "missing", and because human evolution is no longer believed to have occurred in terms of a single linear progression.

Punctuated equilibrium

The theory of punctuated equilibrium developed by Stephen Jay Gould and Niles Eldredge and first presented in 1972 is often mistakenly drawn into the discussion of transitional fossils. This theory, however, pertains only to well-documented transitions within taxa or between closely related taxa over a geologically short period of time. These transitions, usually traceable in the same geological outcrop, often show small jumps in morphology between extended periods of morphological stability. To explain these jumps, Gould and Eldredge envisaged comparatively long periods of genetic stability separated by periods of rapid evolution. Gould made the following observation concerning creationist misuse of his work to deny the existence of transitional fossils:

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. The punctuations occur at the level of species; directional trends (on the staircase model) are rife at the higher level of transitions within major groups.

Evolution as fact and theory

Many scientists and philosophers of science have described evolution as fact and theory, a phrase which was used as the title of an article by paleontologist Stephen Jay Gould in 1981. He describes fact in science as meaning data, not known with absolute certainty but "confirmed to such a degree that it would be perverse to withhold provisional assent". A scientific theory is a well-substantiated explanation of such facts. The facts of evolution come from observational evidence of current processes, from imperfections in organisms recording historical common descent, and from transitions in the fossil record. Theories of evolution provide a provisional explanation for these facts.

Each of the words evolution, fact and theory has several meanings in different contexts. Evolution means change over time, as in stellar evolution. In biology it refers to observed changes in organisms, to their descent from a common ancestor, and at a technical level to a change in gene frequency over time; it can also refer to explanatory theories (such as Charles Darwin's theory of natural selection) which explain the mechanisms of evolution. To a scientist, fact can describe a repeatable observation that all can agree on; it can refer to something that is so well established that nobody in a community disagrees with it; and it can also refer to the truth or falsity of a proposition. To the public, theory can mean an opinion or conjecture (e.g., "it's only a theory"), but among scientists it has a much stronger connotation of "well-substantiated explanation". With this number of choices, people can often talk past each other, and meanings become the subject of linguistic analysis.

Evidence for evolution continues to be accumulated and tested. The scientific literature includes statements by evolutionary biologists and philosophers of science demonstrating some of the different perspectives on evolution as fact and theory.

Evolution, fact and theory

Evolution has been described as "fact and theory"; "fact, not theory"; "only a theory, not a fact"; "multiple theories, not fact"; and "neither fact, nor theory." The disagreements among these statements, however, have more to do with the meaning of words than the substantial issues and this controversy is discussed below.

Evolution

Professor of biology Jerry Coyne sums up biological evolution succinctly:

Life on Earth evolved gradually beginning with one primitive species—perhaps a self-replicating molecule—that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.

This shows the breadth and scope of the issue, incorporating the scientific fields of zoology, botany, genetics, geology, and paleontology, among many others.

But the central core of evolution is generally defined as changes in trait or gene frequency in a population of organisms from one generation to the next. This has been dubbed the standard genetic definition of evolution. Natural selection is only one of several mechanisms in the theory of evolutionary change that explains how organisms historically adapt to changing environments. The principles of heredity were re-discovered in 1900, after Darwin's death, in Gregor Mendel's research on the inheritance of simple trait variations in peas.

Subsequent work into genetics, mutation, paleontology, and developmental biology expanded the applicability and scope of Darwin's original theory.

According to Douglas J. Futuyma:

Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportion of different alleles within a population (such as those determining blood types) to the successive alterations that led from the earliest proto-organism to snails, bees, giraffes, and dandelions.

The word evolution in a broad sense refers to processes of change, from stellar evolution to changes in language. In biology, the meaning is more specific: heritable changes which accumulate over generations of a population. Individual organisms do not evolve in their lifetimes, but variations in the genes they inherit can become more or less common in the population of organisms. Any changes during the lifetime of organisms which are not inherited by their offspring are not part of biological evolution.

To Keith Stewart Thomson, the word evolution has at least three distinct meanings:

  1. The general sense of change over time.
  2. All life forms have descended with modifications from ancestors in a process of common descent.
  3. The cause or mechanisms of these process of change, that are examined and explained by evolutionary theories.

Thomson remarks: "Change over time is a fact, and descent from common ancestors is based on such unassailable logic that we act as though it is a fact. Natural selection provides the outline of an explanatory theory."

Biologists consider it to be a scientific fact that evolution has occurred in that modern organisms differ from past forms, and evolution is still occurring with discernible differences between organisms and their descendants. There is such strong quantitative support for the second that scientists regard common descent as being as factual as the understanding that in the Solar System the Earth orbits the Sun, although the examination of the fundamentals of these processes is still in progress. There are several theories about the mechanisms of evolution, and there are still active debates about specific mechanisms.

There is a fourth meaning for the word evolution that is not used by biologists today. In 1857, the philosopher Herbert Spencer defined it as "change from the homogeneous to the heterogeneous." He claimed (before Darwin) that this was "settled beyond dispute" for organic evolution and applied it to the evolution of star systems, geology and human society. Even Spencer by 1865 was admitting that his definition was imperfect, but it remained popular throughout the nineteenth century before declining under the criticisms of William James and others.

Fact

Fact is often used by scientists to refer to experimental or empirical data or objective verifiable observations. "Fact" is also used in a wider sense to mean any theory for which there is overwhelming evidence.

A fact is a hypothesis that is so firmly supported by evidence that we assume it is true, and act as if it were true. —Douglas J. Futuyma

In the sense that evolution is overwhelmingly validated by the evidence, it is a fact. It is frequently said to be a fact in the same way as the Earth's revolution around the Sun is a fact. The following quotation from Hermann Joseph Muller's article, "One Hundred Years Without Darwinism Are Enough," explains the point.

There is no sharp line between speculation, hypothesis, theory, principle, and fact, but only a difference along a sliding scale, in the degree of probability of the idea. When we say a thing is a fact, then, we only mean that its probability is an extremely high one: so high that we are not bothered by doubt about it and are ready to act accordingly. Now in this use of the term fact, the only proper one, evolution is a fact.

The National Academy of Sciences (U.S.) makes a similar point:

Scientists most often use the word "fact" to describe an observation. But scientists can also use fact to mean something that has been tested or observed so many times that there is no longer a compelling reason to keep testing or looking for examples. The occurrence of evolution in this sense is a fact. Scientists no longer question whether descent with modification occurred because the evidence supporting the idea is so strong.

Stephen Jay Gould also points out that "Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory - natural selection - to explain the mechanism of evolution." These two aspects are frequently confused. Scientists continue to argue about particular explanations or mechanisms at work in specific instances of evolution – but the fact that evolution has occurred, and is still occurring, is undisputed.

A common misconception is that evolution cannot be reliably observed because it all happened millions of years ago and the science therefore is not dependent on facts (in the initial sense above). However, both Darwin and Alfred Russel Wallace, the co-founders of the theory, and all subsequent biologists depend primarily on observations of living organisms; Darwin concentrated largely on the breeding of domesticated animals whereas Wallace started from the biogeographical distribution of species in the Amazon and Malay Archipelago. In the early twentieth century, population genetics had centre stage, and more recently DNA has become the main focus of observation and experimentation.

Philosophers of science argue that we do not know mind-independent empirical truths with absolute certainty: even direct observations may be "theory laden" and depend on assumptions about our senses and the measuring instruments used. In this sense all facts are provisional.

Theory

The scientific definition of the word "theory" is different from the definition of the word in colloquial use. In the vernacular, "theory" can refer to guesswork, a simple conjecture, an opinion, or a speculation that does not have to be based on facts and need not be framed for making testable predictions.

In science, however, the meaning of theory is more rigorous. A scientific theory is "a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses." Theories are formed from hypotheses that have been subjected repeatedly to tests of evidence which attempt to disprove or falsify them. In the case of evolution through natural selection, Darwin conceived the hypothesis around 1839, and made a first draft of the concept three years later in 1842. He discussed this widely with many of his intellectual companions, and conducted further research in the background to his other writings and work. After years of development, he finally published his evidence and theory in On the Origin of Species in 1859.

The "theory of evolution" is actually a network of theories that created the research program of biology. Darwin, for example, proposed five separate theories in his original formulation, which included mechanistic explanations for:

  1. populations changing over generations
  2. gradual change
  3. speciation
  4. natural selection
  5. common descent

Since Darwin, evolution has become a well-supported body of interconnected statements that explains numerous empirical observations in the natural world. Evolutionary theories continue to generate testable predictions and explanations about living and fossilized organisms.

Phylogenetic theory is an example of evolutionary theory. It is based on the evolutionary premise of an ancestral descendant sequence of genes, populations, or species. Individuals that evolve are linked together through historical and genealogical ties. Evolutionary trees are hypotheses that are inferred through the practice of phylogenetic theory. They depict relations among individuals that can speciate and diverge from one another. The evolutionary process of speciation creates groups that are linked by a common ancestor and all its descendants. Species inherit traits, which are then passed on to descendants. Evolutionary biologists use systematic methods and test phylogenetic theory to observe and explain changes in and among species over time. These methods include the collection, measurement, observation, and mapping of traits onto evolutionary trees. Phylogenetic theory is used to test the independent distributions of traits and their various forms to provide explanations of observed patterns in relation to their evolutionary history and biology. The neutral theory of molecular evolution is used to study evolution as a null model against which tests for natural selection can be applied.

Evolution as theory and fact in the literature

The following sections provide specific quotable references from evolutionary biologists and philosophers of science demonstrating some of the different perspectives on evolution as fact and theory.

Evolution as fact

  • American zoologist and paleontologist George Gaylord Simpson stated that "Darwin... finally and definitely established evolution as a fact."
  • Hermann Joseph Muller wrote, "So enormous, ramifying, and consistent has the evidence for evolution become that if anyone could now disprove it, I should have my conception of the orderliness of the universe so shaken as to lead me to doubt even my own existence. If you like, then, I will grant you that in an absolute sense evolution is not a fact, or rather, that it is no more a fact than that you are hearing or reading these words."
  • Kenneth R. Miller writes, "evolution is as much a fact as anything we know in science."
  • Ernst Mayr observed, "The basic theory of evolution has been confirmed so completely that most modern biologists consider evolution simply a fact. How else except by the word evolution can we designate the sequence of faunas and floras in precisely dated geological strata? And evolutionary change is also simply a fact owing to the changes in the content of gene pools from generation to generation."

Evolution as fact and theory

Fact is commonly used to refer to the observable changes in organisms' traits over generations while the word theory is reserved for the mechanisms that cause these changes:

  • Writing in 1930, biologist Julian Huxley entitled the third book of the wide-ranging series The Science of Life, which dealt with the fossil record and the evidence of plant and animal structures, The Incontrovertible Fact of Evolution. He also says "Natural Selection...is not a theory, but a fact. But does it...suffice to account for the whole spectacle of Evolution?...There we come to speculative matter, to theories." But he concludes that "the broad positions of Darwinism re-emerge from a scrutiny of the most exacting sort essentially unchanged." In 1932, a portion of the book was republished under the title Evolution, Fact and Theory.
  • Stephen Jay Gould writes, "...evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered."
  • Similarly, biologist Richard Lenski says, "Scientific understanding requires both facts and theories that can explain those facts in a coherent manner. Evolution, in this context, is both a fact and a theory. It is an incontrovertible fact that organisms have changed, or evolved, during the history of life on Earth. And biologists have identified and investigated mechanisms that can explain the major patterns of change."
  • Biologist T. Ryan Gregory notes, "biologists rarely make reference to 'the theory of evolution,' referring instead simply to 'evolution' (i.e., the fact of descent with modification) or 'evolutionary theory' (i.e., the increasingly sophisticated body of explanations for the fact of evolution). That evolution is a theory in the proper scientific sense means that there is both a fact of evolution to be explained and a well-supported mechanistic framework to account for it."

Evolution as fact and not theory

Other commentators – focusing on the changes in species over generations and in some cases common ancestry – have stressed, in order to emphasize the weight of supporting evidence, that evolution is a fact, arguing that the use of the term "theory" is not useful:

  • Richard Lewontin wrote, "It is time for students of the evolutionary process, especially those who have been misquoted and used by the creationists, to state clearly that evolution is fact, not theory."
  • Douglas J. Futuyma writes in Evolutionary Biology (1998), "The statement that organisms have descended with modifications from common ancestors—the historical reality of evolution—is not a theory. It is a fact, as fully as the fact of the earth's revolution about the sun."
  • Richard Dawkins says, "One thing all real scientists agree upon is the fact of evolution itself. It is a fact that we are cousins of gorillas, kangaroos, starfish, and bacteria. Evolution is as much a fact as the heat of the sun. It is not a theory, and for pity's sake, let's stop confusing the philosophically naive by calling it so. Evolution is a fact."
  • Neil Campbell wrote in his 1990 biology textbook, "Today, nearly all biologists acknowledge that evolution is a fact. The term theory is no longer appropriate except when referring to the various models that attempt to explain how life evolves... it is important to understand that the current questions about how life evolves in no way implies any disagreement over the fact of evolution."

Evolution as a collection of theories not fact

Evolutionary biologist Kirk J. Fitzhugh writes that scientists must be cautious to "carefully and correctly" describe the nature of scientific investigation at a time when evolutionary biology is under attack from creationists and proponents of intelligent design. Fitzhugh writes that while facts are states of being in nature, theories represent efforts to connect those states of being by causal relationships:

"'Evolution' cannot be both a theory and a fact. Theories are concepts stating cause–effect relations. Regardless of one's certainty as to the utility of a theory to provide understanding, it would be epistemically incorrect to assert any theory as also being a fact, given that theories are not objects to be discerned by their state of being."

Fitzhugh recognizes that the "theory" versus "fact" debate is one of semantics. He nevertheless contends that referring to evolution as a "fact" is technically incorrect and distracts from the primary "goal of science, which is to continually acquire causal understanding through the critical evaluation of our theories and hypotheses." Fitzhugh concludes that the "certainty" of evolution "provides no basis for elevating any evolutionary theory or hypothesis to the level of fact."

Dr William C. Robertson writing for National Science Teachers Association writes, "I have heard too many scientists claim that evolution is a fact, often in retort to the claim that it is just a theory. Evolution isn’t a fact. Rather than claiming so, I think scientists would be better served to agree that evolution is a theory and then proceed to explain what a theory is -- a coherent explanation that undergoes constant testing and often revision over a period of time."

Related concepts and terminology

The main purpose of evolutionary biology is to provide a rational explanation for the extraordinarily complex and intricate organization of living things. To explain means to identify a mechanism that causes evolution and to demonstrate the consequences of its operation. These consequences are then the general laws of evolution, of which any given system or organism is a particular outcome.

Graham Bell, Selection: The Mechanism of Evolution (2008)

  • "Proof" of a theory has different meanings in science. Proof exists in formal sciences, such as a mathematical proof where symbolic expressions can represent infinite sets and scientific laws having precise definitions and outcomes of the terms. Proof has other meanings as it descends from its Latin roots (provable, probable, probare L.) meaning 'to test'. In this sense a proof is an inference to the best or most parsimonious explanation through a publicly verifiable demonstration (a test) of the factual (i.e., observed) and causal evidence from carefully controlled experiments. Stephen Jay Gould argued that Darwin's research, for example, pointed to the coordination of so many pieces of evidence that no other configuration other than his theory could offer a conceivable causal explanation of the facts. In this way natural selection and common ancestry has been proven. "The classical proof is the improvement of crops and livestock through artificial selection." Natural selection and other evolutionary theories are also represented in various mathematical proofs, such as the Price equation. To remain consistent with the philosophy of science, however, advancement of theory is only achieved through disproofs of hypotheses.
  • "Models" are part of the scientific or inferential "tool-kit" that are constructed out of preexistent theory. Model-based science uses idealized structures or mathematical expressions to strategically create simpler representations of complex worldly systems. Models are designed to resemble the relevant aspects of hypothetical relations in the target systems under investigation.
  • "Validation is a demonstration that a model within its domain of applicability possesses a satisfactory range of accuracy consistent with the intended application of the model." Models are used in simulation research. For example, evolutionary phylogeneticists run simulations to model the tree like branching process of lineages over time. In turn, this is used to understand the theory of phylogenetics and the methods used to test for relations among genes, species, or other evolutionary units.

Samaritans

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