User:Silence/Creationism

What is evolution?
In biology, evolution is the change in a population's inheritable traits from generation to generation. It boils down to 4 core ideas:
 * 1. Heredity. Parents pass on their traits to offspring.
 * 2. Variation. Offspring differ slightly from their parents, and from each other.
 * 3. Fitness. Some of these differences are more helpful for reproducing than others.
 * 4. Selection. Offspring with more helpful traits will in turn have more offspring, making the traits more common in the population.

Over time, this simple process of small incremental changes can have dramatic results. As traits become more common or rare in the population over millions of years, a species gradually changes, either randomly or by the environment's selection of certain helpful traits, into a new species&mdash;or branches off into several. This process is called speciation.

Charles Darwin noted all of these processes in his 1859 book, On the Origin of Species. Darwin convinced the scientific community, through a wealth of biological evidence from around the world, that this process could explain the astonishing diversity of life. He coined the term "natural selection," in contrast with man-made "artificial selection" (i.e., breeding), and argued that the similarities between all living things could be accounted for with evolution: birds, for example, don't just happen to all have feathers; they have feathers because they all descend from a common ancestor with feathers, and simply retained that useful trait over the years. Noting that all living things have varying degrees of similarity, Darwin posited that all life, if given enough time to repeatedly diverge, could develop from a single common ancestor into the wealth of species known today. Thus, all organisms are related.

Darwin's mechanism for evolutionary change has been heavily modified and fleshed out since his day. In the early 20th century, the rediscovery of Gregor Mendel's experiments showing that organisms' traits are passed on to offspring in discrete (i.e., non-"blending") units, called "genes," led to the modern theory of evolution, called the Neo-Darwinian Synthesis. By the 1950s, the physical basis for inheritance was finally understood as large, self-replicating molecules of nucleic acid, called DNA.

How does heredity work?
The body's many functions are produced by tiny molecular machines called proteins, which behave in a variety of different ways depending on their shape. Proteins consist of chains of amino acids, and their shape is determined by the particular sequence of acids, which causes the molecule to consistently "fold" into intricate structures. Each protein can be viewed as a causally active "sentence"; the roughly 20 different kinds of amino acids used are the available "words," which are each produced by three-"letter" words in DNA&mdash;the word AUG, for example, always produces the amino acid methionine. To limit each sentence's size, a few words, such as "TAA," act as "periods" which end each protein chain and allow the next protein to be begun. Thus, all the complexity of proteins is the result of different sequences of three-letter words in DNA, with the alphabet of four available letters (A, G, C, and T) physically consisting of molecules which form stable pairings and are held in place on either side by a "backbone" of sugar and phosphate.

Structures in the cell, such as RNA, naturally generate proteins from DNA, by virtue of their chemical composition; thus, differences in the DNA will result in different proteins, which will change the structure and function of the organism as a whole. In this way, an observable trait can be dependent on a particular region of functional DNA, called a gene. Inheritable traits are passed on with the complete set of genes, called the "genome," when an organism replicates its DNA during reproduction. Because DNA replication is almost perfect, organisms closely resemble their parents, with sexual organisms exhibiting more variability due to borrowing a random half of their genomes from each parent.

Where does variation come from?
Most human DNA is non-coding, amounting to gibberish "words" which don't build viable proteins. However, when mutations&mdash;relatively rare errors due to DNA miscopying or outside influences&mdash;cause some letters to be altered or moved around, brand-new protein "sentences" can be formed by the new sequence. This can have disastrous effects if mutations occur in a gene coding for an important protein; however, most mutations are harmless, only affecting redundant or nonfunctional areas of DNA. Since selection will "weed out" organisms with bad mutations, but will permit neutral ones to accumulate, over time many random mutations can radically reshape the genome of a species, while only occasionally producing actual observable effects.

Once genetic variation is introduced, it can become more common or rare in a population through drift (which is random), or through selection (which is nonrandom). In selection, a trait that assists in individual survival and reproduction will tend to become more common because more copies of that trait, encoded in DNA, will be passed on to the next generation; conversely, harmful traits will tend to become rarer. Eventually, a trait can reach 100% frequency&mdash;or it can vanish entirely. What keeps populations evolving indefinitely, aside from random mutation, is the fact that environments change over time, which in turn changes which traits are advantageous. Thus, fitness is always situational; what works in one context won't work in another.

A consequence of this is that evolution is not progressive or directional&mdash;there is no overarching "goal" of evolution. Indeed, evolution often reverses itself or reduces complexity, usually to save energy being used by unnecessary structures. Vestigial (i.e., "trace") structures, such as the human appendix (formerly used for digesting cellulose), have lost most or all of their original functions.

How do species split?
If a population splits into isolated subpopulations, each diverging in a different direction, eventually these groups can lose the ability to breed with each other, becoming separate species. This process, cladogenesis, is what allows the number of species to increase.

A species is a group of organisms that can successfully interbreed. However, this definition is often problematic in practice, because some closely-related species can breed with varying degrees of success. Horses and donkeys can reproduce to make mules, but these offspring are sterile. Even more ambiguous are ring species (e.g., Larus gulls and Ensatina salamanders), geographically adjacent populations which have migrated in a circle (e.g., around a mountain) to form a "ring," where every population is similar enough to its neighbors to interbreed, but by the time the ring is completed, the two ends of the ring are so different that they can no longer reproduce. This demonstrates that speciation is a gradual occurrence, and only after-the-fact, when populations have spent enough time in reproductive isolation from each other, can they be clearly designated as separate species.

The cause of this inability to interbreed is the accumulation of mutations. After over 5 million years of mutation and isolation, humans and chimpanzees are unable to breed with each other despite sharing over 98% of their genomes in common. The most dramatic mutation in this interim has been the fusing of two chimpanzee chromosomes (bundles of DNA) into one human chromosome (Chromosome 2), resulting in chimpanzees having 24 pairs of chromosomes while humans have 23.

Evidence of evolution
Demonstrations of day-to-day evolution are omnipresent. Any example of populations changing genetically, be they dog breeds or human races or virus strains, is a true example of evolution. Indeed, the only reason new flu shots are needed each year is because influenza strains evolve so rapidly that targeted vaccines become rapidly out-of-date.

However, in this context creationists often appeal to the distinction between "microevolution" and "macroevolution," the latter being "large-scale" evolution, at or above the species level. Sophisticated creationists will claim to support the former while rejecting the latter, in order to sidestep obvious examples such as dog breeds. In modern biology, this distinction is basically seen only as one of timescale: the processes of "micro" and "macro" are the same, as macro is essentially just "a lot of micro." Additionally, macroevolution has been directly observed just as microevolution has&mdash;speciations have been observed in maize, mice, mosquitoes, fruit flies, algae, etc.

Creationists often respond by moving the goalposts, trying to redefine "macroevolution" as even 'bigger' change (fish giving birth to monkeys??!). Since dramatic evolution typically takes millions of years, it is unreasonable to demand direct demonstrations of historical evolutionary changes. However, immensely powerful indirect evidence for the evolutionary history and common descent of species can be found in the fossil record, and in anatomical and molecular similarities between species (homologies).

Evidence of common descent
Fossilization is an extremely rare process. It requires the convergence of numerous different factors at once, such as rapid burial (e.g., by rockslide) to prevent decay, and a conducive climate. Thus, the fossil record, although large, only represents a small fraction of the total number of species that have lived. Moreover, some species, such as ones without hard body parts, naturally tend to fossilize less often.

Despite these qualifications, the fossil record provides powerful evidence of evolutionary history. Because rock strata correspond chronologically to geologic periods, with more recent fossils buried above more ancient ones, it is possible to repeatedly test evolution by determining whether species are arising in the orderly way predicted by evolution&mdash;with complex creatures only after simpler ones, terrestrial animals only after aquatic ones, etc. In some cases, the fossil record has so few gaps that near-complete lineages can be reconstructed, as for the horse. Thousands of hominid fossils have been discovered, illustrating sister and parent species of modern humans.

The similarities between living species is also dramatic confirmation of evolution. Without common descent, there is no reason to expect a hierarchical distribution of traits&mdash;birds should be just as likely as mammals to have fur or breasts or live young, and we should not be surprised to see ostriches with tentacles or lions with scales, since there is no necessary reason for species with one trait in common (e.g., feathers) to consistently have anything else in common (e.g., hollow bones and egg-laying). Evolution is the only explanation for this ordered distribution of traits: It points out that, just as the similarities humans are born with can be explained by all humans having a common ancestor, so too can the similarities between humans and other species be easily explained by positing more distant common ancestors with those species.

Although anatomy and fossils have borne out evolutionary theory perfectly, the truly astonishing confirmation of evolutionary biology only came with the advent of molecular biology, which revealed that even on a biochemical level species have countless arbitrary similarities. And for the exact same reason that DNA testing on humans is seen as valid evidence for family relationships, so too is it used to reconstruct the family trees between different species. In addition to the countless correspondences between functional genes, genomes feature numerous redundant and nonfunctional segments, which are also shared between closely related species. Endogenous retroviruses, which implant themselves in DNA and using the host organism to replicate themselves, are found in the exact same locations on the genome of related species.

Non-evolution
When macroevolution too has been demonstrated, creationists often move the goalposts again, demanding evidence for the origins of life, the universe, and everything.

Evolutionary biology does not cover any of these areas. Moreover, the mere fact that something is not fully understood is not a reason to reject scientific efforts altogether. Creationism is not vindicated every time biologists or astrophysicists can't explain something; to truly make their case, creationists must put forward positive, conclusive evidence for their own world-view. In fact, even if evolution was refuted entirely, the wealth of other possible options means that creationism (and even more so Biblical creationism) would still just be one contender among many.