Adaptation
An adaptation is a positive characteristic of an organism that has been favored by natural selection. The concept is central to biology, particularly in evolutionary biology. The term adaptation is also sometimes used as a synonym for natural selection, but most biologists discourage this usage.
Adaptation is the change in organisms that allow them to live successfully in an environment.  Adaptations enable living  organisms to cope with environmental stresses and pressures.   Adaptation can be structural or behavioral. Structural adaptations are special body parts of an organism that help it to survive in its natural habitat (e.g., skin colour, shape, body covering). Behavioural  adaptations are special ways a particular organism behaves to survive in its natural habitat. Physiological adaptations are systems present in an organism that allow it to perform certain biochemical reactions (e.g., making venom, secreting slime, being able to keep a constant body temperature).
Adaptations are traits that have been selected for by natural selection.  The underlying genetic basis for the adaptive trait did not arise as a consequence of the environment; the genetic variant pre-existed and was subsequently selected because it provided the bearer of that variant some advantage.  The first experimental evidence of the pre-existing nature of genetic variants was provided by Joshua Lederberg and colleagues who developed fluctuation analysis, a method to show the random fluctuation of pre-exisitng genetic changes that conferred resistance to antibiotics by the bacterium Escherichia coli
While many traits have obvious adaptive purposes, it is worthwhile to point out that many traits are not adaptive, that is, there is no obvious reason scientists can divine for the presence of a certain trait.  This situation is common and there are many causes: the utility of a trait is lost and hence does not now appear adaptive, the utility of a trait is unknown, the trait is a consequence of another trait that is adaptive (the Spandrel idea).  This observation underscores two other important points: genetic variants arise randomly and hence traits can appear randomly and that because the environment for all living things is constantly in flux, the utility of adaptations will naturally ebb and flow.
Organisms that are not suitably adapted to their environment will either have to move out of the habitat or die out. The term die out in the context of adaptation simply means that the death rate over the entire species (population, gene pool ...)  exceeds the birth rate for a long enough period for the species to disappear; due to individual phenotypic plasticity, individuals will be more or less successful. The opposite is selection which in this context means that the birth rate of those carrying the adaptive trait and the hence the underlying genetic variant exceeds over time the birth rate of those that do not carry the adaptive traitTemplate:Unicode.

# Adaptation vs. adaptiveness
A trait being adaptive, i.e. increasing the organism's fitness, is neither a necessary nor sufficient condition for it to be an adaptation. Of course, an adaptation must have been adaptive at some point in an organism's evolutionary history, but such an organism's environment and ecological niche can change over time, leading to adaptations becoming redundant or even a hindrance (maladaptations). Such adaptations are termed vestigial.

# Adaptation vs. acclimation
There is a great difference between adaptation and acclimation. Adaptation occurs over many generations; it is a gradual process caused by natural selection. Acclimatization generally occurs within a single lifetime and copes with issues that are less threatening. For example, if a human was to move to a higher altitude, respiration and physical exertion would become a problem, but after spending time in high altitude conditions one may acclimate to the pressure and function and no longer notice the change. This ability to acclimate is an adaptation, but not the acclimation itself.
A counter-adaptation is an adaptation that has evolved due to the selective pressure of another adaptation. This occurs in an evolutionary arms race, where a new adaptation giving one species an advantage is countered by the appearance and spread of a new feature that reduces the effectiveness of the first adaptation.

# Theories
The theory of adaptation was first put forth by Jean-Baptiste Lamarck. His theories are also referred to  as the inheritance of acquired traits.
Lamarck's theory was for a time held as an alternative scientific explanation for evolutionary change observed by Darwin in the The Origin of Species. The classic giraffe analogy offers the best delineation between the two.
- According to Darwin, more long-necked giraffes reproduce than short-necked giraffes and as such giraffes today have long necks.
- According to Lamarck, it was giraffes stretching their necks in response to higher leaves that resulted in giraffes having long necks. (This trait being passed on to the next generation)
Although neither theory in its conception could provide a complete description of the mechanism of transmission of trait variation (i.e., particulate inheritance), many recognized Darwin's theory immediately upon publication as a more complete and empirically supported theory.  Modern genetics have since established the fundamental implausibility of Lamarckian inheritance, due to the one-way nature of transcription.  However, see epigenetics and Baldwinian evolution for analogous processes in modern evolutionary theory.