User:TomS TDotO/Sandbox

Random
===Naturalism vs. Supernaturalism How do the natural and the supernatural differ in their treatment of the random? One way of distinguishing the natural from the supernatural is that the natural follows the "laws of nature". Natural objects tend to operate within limits. In the formative stages of modern science, the material world was thought of as deterministic. That is challenged by Quantum Mechanics and Complexity Theory, but still there are limits. The quantum uncertainty of the momentum, Δp, and of position,  Δq, are related by Heisenberg's Uncertainty: $$ \Delta p \Delta q \geq \frac{\hbar}{2} $$. In brief, there is law-like behavior. If one tosses an unbiased coin, one can reasonably expect it to land "heads" or "tails" of similar frequency (or some small chance for on the edge). But if we allow the supernatural, "anything goes". If one is using telekinesis, or prayer, then there is no such thing as a fair bet. Ironically, those w

Contradictions
Not so incidentally, the Bible does not make the claim that the narrative of Genesis is eyewitness testimony.

Myth of Persephone
The Myth of Persephone provides an explanation for the changes of seasons: why the ground does not produce adequate food crops through the Winter.

The story is told in various forms, one of them being, in outline, that the goddess Persephone, daughter of Demeter, the goddess of cereal grains, what kidnapped by Hades, the god of the Underworld, to be his queen. Demeter, in mourning for her missing daughter, neglects the flourishing of the grains. When Demeter discovers that Persephone is Queen of the Underworld, she bargains with Hades for her return. Hades relents with the proviso that Persephone cannot leave if she has tasted any of the food of the Underworld. As it turns out, she has eaten a single pomegranate seed. The best that Demeter can hope for is that Persephone leave the Underground for temporary stays of part of each year. Thus Demeter is happy to have her daughter with her, and the crops flourish, but when winter comes, Persephone must return to the Underworld and crops die away.

This provides an example of a supernatural explanation for a natural event. It gives an accounting for why the seasons, rather than crops flourishing all year around (and why not always barren ground). It passes the criterion of Falsifiability, for the explanation fails when confronted with new data, unknown to the world in which the myth was told, that there are opposite seasons in the antipodes (and a totally different pattern of seasons in the tropics). It connects properties of the factors providing the explanation (the emotions of Demeter, the laws of Hades) with the result being explained (the growth of crops, the part-time nature of seasons).

Own goal
A player helps the opposing team by scoring in one's own goal , the goal that player's team is defending. Excluding the possibility of throwing the game, this presumed to be by accident, an unforced error. The metaphorical use of the expression is expressed by other metaphors drawn from fields of combat: shooting oneself in the foot  and friendly fire . This article is concerned with its application to argument, when the proponent of one side makes an argument which (again, presumedly by inadvertence rather than design) tends to hurt the side being defended (or helps an opponent).

Unintentional apophasis
One should distinguish "One Own's Goal" in the narrow sense from the species of literary irony, unintentional apophasis. As in Shakespeare's Hamlet, when Hamlet's mother, Queen Gertrud, is seen as (inadvertently, indeed unconsciously and uncomprehendingly) calls to mind to her own behavior when she says, the lady dost protest too much. Thus, too, the inept debater doesn't realize that mention of a certain thing calls to mind a strength of the opponent. ([Intentional] apophasis is the figure of rhetoric where one brings up a topic by feigning not to mention it. (For example,"I will not say anything about my opponent being an atheist"

Thus, when a backer of "Intelligent Design" is complaining about the physics of the multiverse says, "A hypothesis with no evidence to speak of, whose supporters nevertheless feel a burning need for it to be true. What does that remind you of?"

Or when we are invited to wonder why a single cause does not produce a single product: "And why did evolution divert in so many directions--birds, fish, elephants, apes, humans--if there is some force evolving to the maximum? Why isn't everything a human--a superior human?"

Behe's Tic
Because of the frequency that it appears in the work of Michael Behe, it carries the name Behe's Tic. Thus, when Behe, in "The Edge of Evolution" discusses how (1) the evolutionary change, sickle cell anemia, has remained effective against malaria, while (2) all products of human design combatting malaria eventually have been made ineffective by evolution in the malaria parasite. One immediately thinks of Orgel's Second Rule: "Evolution is cleverer than you are."


 * "If the "ditch" were actually a canyon 100 feet wide, however, you would not entertain for a moment the bald assertion that he jumped across." (Darwin's Black Box, page 13) So, the reader thinks, for how many moments would one entertain the bald assertion without any details that an "Intelligent Designer" was responsible?


 * "If a theory claims to be able to explain some phenomenon but does not generate even an attempt at an explanation, then it should be banished." (page 186) It seems counter-productive to remind the reader of the long-standing complaint about creationism not making such an attempt.


 * In his testimony as an expert witness in the Dover ID trial he said, "Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well." Aside from the embarrassment of mentioning astrology ...

Social Darwinism
The name "Social Darwinism" seems to have been coined by non-scientists looking for a name for a social-political movement of the early 20th century. But the name has been taken seriously, and maliciously extended to Hitler and the Nazi party as an attack on evolutionary biology, and identifying evolution with Darwin's mechanism of differential reproductive success working on non-directed variations ("natural selection"). The irony in this is that it is
 * creationism, not evolution, which identifies "better" or "worse"
 * creationism, not evolution, which says that without purposeful direction (aka intelligent design) a lineage will suffer deterioration
 * these various political movements grew in the era (about 1900-1940) known as the "eclipse of darwinism", when, even among scientists, the power of natural selection was not appriated, in favor of various directional forces were sought out. (Note that Henri Bergson, the proponent of élan vital was awarded the Nobel Prize for Literature in 1927, and the Grand Cross of France's Legion of Honor in 1930.)
 * Darwin and even evolution were ignored, or even singled out for derision, by the leaders of these movements
 * some sort of mysticism, if not conventional religion, was popular within some of these movements, as well as pseudoscience

If it weren't for the misnomer "Social Darwinism", these movements would be an embarrassment, something ignored, or, more honestly to be excused, if not apologized for, by creationists.

Self contradiction
Yet another species of self-inflicted trouble is when two arguments, not usually associated together, conflict with one another. This can be called, in reference to "arguing in a circle", rather "arguing around a Möbius strip". (When one travels around a Möbius strip, one ends up upside down from the starting position.) It is also called locally consistent (that is, only locally, rather than the usually valued globally consistent), and attributed to a short attention span", or, less charitably, immediate gratification'''.

Hydrologic sorting
That aspect of Young Earth Creationism which takes as literal historical reality the Biblical story of Noah's Ark and the Deluge may account for animal fossils as being laid down over the geological short time of less than a year. The ordering of the fossils as explained by geologists as being a record, over many years, of the differences in fauna. Some of the Flood Geologists say that hydrological sorting (other suggestions are sorting according to the agility of animals in - temporally escaping the rising Flood, or according to ecological zonation) would produce an ordering of the carcases drowned by the Flood. This contradicts the standard contention by creationists that (their understanding of) the Second Law of Thermodynamics prevents the appearance of order without the direction of a purposeful agency.

In the proper (or narrow) sense
Among the arguments which are of contrary effect in the case of opponents of the science of evolutionary biology. They actually are arguments against what they are supposed to be supporting. They score a goal for their opponent.

The fallacy of disanalogy
Paley's famous analogy of design notes that one infers design from the complexity of a watch, and notes that the world of living things are also complex, which should lead to to expect design.
 * How can we expect to travel a mile a second? No human has ever run a mile in even one minute. Therefore, the solution to traveling a mile a second is by running.
 * Dale wants to lose weight, but has had no success in several of the latest fad diets. Therefore, reasons Dale, the way to lose weight is to be found in this new fad diet.
 * The pyramids of Mesoamerica where built a thousand or more years later than the Egyptian pyramids, and were built out of different materials, in a different shape, for different purposes. Therefore, the pyramids of Mesoamerica were built by ancient Egyptians.

Whatever the merits of that analogy, some advocates of ID/C ruin the argument by talking too much. The analogy becomes: one observes that the smartest scientists have not been able to approach the construction of the simplest of living things; and therefore living things must, all the more so, be designed. That is, as if it needs to be pointed out, the analogy is with what we have no idea of its being capable of being design to the conclusion that it must be designed. Rather, the more obvious analogy is: Because we don't have any idea of how to design it, it just might not be designed.

A work of art can be distinguished from a natural object
If a naive newcomer to the area of Mount Rushmore might wonder where the famous sculptures of four U.S. Presidents came from. But any reasonable person sees clearly that the sculptures are markedly different in their appearance from the natural world. This, so we are told, justifies the similar conclusion that living things are also designed. The conclusion is that the flora and fauna on Mount Rushmore are designed, just as the sculptures are designed. Which means that, in the respect that they are designed, we cannot distinguish between the sculptures and something which grew there. The "sophisticated" person who informs the "naive" person that the sculptures are desiged, just like a bird or a moss, has not been informative.⅜

Theory and fact
Often one hears it said that evolution is both a theory and a fact.

Evolution is commonly defined in biology as the change in the hereditary makeup of populations, or, in Darwin's phrase, "descent with modification". Thus evolution is a process, something that happens in the world of life which can be observed taking place and measured, replicated under controlled conditions in the lab and freely happening in the wild, and, as far as we can tell, has been happening as long as there has been life on earth and wherever we look. It's fair to say that it is a fact.

Evolution forms a critical ingredient in theories which explain many aspects of the variety of life. There is no known explanation for the "tree of life" which does not involve descent with modification from common ancestors. A theory invoking evolution to explain things can be called a "theory of evolution". In this sense a theory of evolution is like a theory of gravitation in which gravity explains the fact that planets orbit the sun. Evolution explains, and in that sense evolution is a theory. See also germ theory.

Also, the fact that evolution happens and how it happens begs for a theory of evolution. It's too complex to be just a matter of chance. Much as the fact that things fly is explained by a theory of flight. Although nobody says that flight is a theory. See also theory of everything.

Medieval arguments against geocentrism
John Buridan considered the motion of the Earth, but decided against it. But he did propose an argument against the center of the universe being the center of the Earth (that, after all, is the literal meaning of "geocentrism"). He observed that the Earth is not symmetrical, with land predominates in one hemisphere (his own) and water in the antipodes. Then, when there is erosion of land into the water, there is a shift in the location of the center of gravity of Earth, which, if the center of gravity of the Earth was the center of the universe, would require a motion of the Earth to compensate for the change.

Early modern arguments against geocentrism
Pre-modern geocentrism was eliminated by a combination of factors. It wasn't just a matter of the computations of motions.

The earth is not special
One of the major factors was the recognition that there was not a difference in kind between the world beneath the Moon and the heavenly bodies. It had been believed that the planets were made of something different (a quintessence, rather than the four elements of earth, air, fire, and water) which was perfect and unchanging, which naturally moved in circles rather than straight lines. (Although it had long been recognized that the physical explanation, that the planets were carried by spheres, fell afoul of the geometrical observation that spheres had to intersect.) But the telescope showed that the Moon had mountains and might be rather more like the Earth than had been contemplated before; that the Sun had spots which changed; Venus showed phases; Jupiter had its own moons; and there were no spheres which carried the planets. (Today, with the rockets exploring the planets, we have much more obviously seen that Mars, the Moon, and a comet have a landscape made up of the same kinds of elements as the Earth which can be explored by rovers working as they do on earth, rockets made of terrestrial materials travel through interplanetary space following the same rules as the planets and meteorites were formerly celestial objects.) Why, then, should we believe that there is anything different about the planets? Why should they be subject to forces that carry them in a daily orbit around the earth, which the Earth somehow resists? Where can we find the boundary between those bodies which are participating in this daily rotation and the fixity of the Earth? Crossing the transition between Earth and space is now a commonplace with no perception of a discontinuity. The Earth's gravity, magnetism, light, radio waves and atmospheric gases trail off gradually into space. What - and where - stops the rotary forces from acting on the Earth?

There are many centers of orbits
Another telling discovery was of the satellites of Jupiter. Jupiter was seen to be another center of motion. The Earth was not the only center of motion. Tycho Brahe's model (which is the model favored by many modern geocentrists) had the Sun as a center of motion for Mercury, Venus, Mars, Jupiter and Saturn. This is already making things complicated. It is one thing to take the Earth as a unique center of motion, but now we're getting multiple centers of motion, with no particular reason for why the Moon, the Sun, and (maybe the "fixed stars") orbiting the Earth; while the five other planets (with more to come) orbiting the Sun; and Jupiter (and, again, more to come) being the center of motion for other bodies. (Today, we have interplanetary rockets changing their centers of motion - starting off with being Earth orbiters, then becoming Sun orbiters, and then orbiting their destination planets (which may be more than one). This is all very odd under a geocentric model.

The motions of the distant stars
When we describe the geocentric motion of the stars, we are constantly referring back to their relationship with the Earth. Take one example, Polaris, situated (today) just about exactly over the North Pole of the Earth.

Simply saying that the earth is not rotating does not give an adequate description of the rotation of the heavens, for there is a complex relation between the geocentric motion of the sun and that of the stars. Most significantly, the sun has a seasonal motion along the Zodiac (from a heliocentric point of view, the earth orbits the sun once a year) which is the reason for the change in hours of daylight, and which is the basis for astrological "sun signs" (if you're an Aries, you don't believe this). When one object revolves around another, it makes an additional rotation, so while the year has 365+ "solar days", it has 366+ "sidereal (stellar) days"; or to put it a different way, a sidereal day is about 4 minutes shorter than a solar day. There is also a small difference between the Zodiac and the stars, what is called a sideral day is actually based on the Zodiac, while there is a stellar day which is based on the "fixed stars". Thus there are three possible "days": a solar day, where the sun revolves around the earth 360 degrees; a sidereal day, where the "first point of Aries" revolves around the earth; and the stellar day, where the stars revolve around the earth.


 * solar day = day&#9737; = 24x60x60 seconds
 * sidereal day = day&#9800; = 86,164.09053 seconds (vernal equinox day)
 * stellar day = day&#9733; = 86,164.099 seconds (1 rotation of "fixed" stars)

These "days" are of interest for the analysis of geocentrism when the length of the daily path of distant objects may be longer than one light-day; one light-day is the distance that light travels in one day; and thus an object which moves through a path longer than one light-day per day is moving faster than the speed of light. Introduce this notation:


 * lt-day&#9733; = light-day (stellar)
 * lt-day&#9737; = light-day (solar)
 * lt-day&#9800; = light-day (sidereal)

&#322;t-day (or -hour or -year) = lt-day / 2&#960; = radius of circle with circumference lt-day. (The bar through the &#320;, as in the constant &#295;, indicating divison by 2&#960;.)


 * &#322;t-day&#9737; ~ 4.122 442 2 x 1012 meters
 * &#322;t-day&#9800; ~ 4.111 186 1 x 1012 meters
 * &#322;t-day&#9733; ~ 4.111 186 5 x 1012 meters

CreationWiki makes a number of suggestions in conflict with geocentrism - in particular that the Earth does not have a daily revolution - a couple of which are not quite as simple as they seem.

One is the remark that certain earth-centered events, such as major earthquakes, make a difference in the length of the day. This is easy to understand in a model in which the earth is rotating and is affected by such an event, but it is difficult to understand how the motions of the heavens are everywhere changed immediately by an event on the earth. Unfortunately, the magnitude of these effects appears to be below the level at which they can be reliably detected - a matter of a few microseconds in the length of the day, while the best measurements can only detect changes of the order of ten microseconds or so. Until chronometry is improved, there is not clear experimental evidence for the effect.

Another case is the rotation of the heavens at speeds faster than the speed of light. At first glance, it seems an open-and-shut case that stars at the distances of light years must be traveling at speeds much greater than the speed of light if they orbit the earth in a day (or in any time less than years). However, the distances to stars are determined basically by their annual parallax, and thus rely on the assumption that the earth is in a yearly orbit around the sun. The case can be made, just barely, within the solar system. The distances to the planets traditionally have been based on Earth-based triangulation of the distance to Venus at the rare transits of Venus. But Venus is not far enough to present the "faster than the speed of light" problem. For that, we must go out to Neptune and beyond, and there is a complicated chain of inference which also involves assumptions about the speed of light beyond the Earth. The exploration of the solar system by rocket probes bypasses these complications, for the distance of the probes can be directly observed as the delay of the radio signals, in units directly related to the speed of light: for example, light hours. Voyager 1 and Voyager 2 present the best examples. The calculations are straightforward, with the only complication being that these objects are not directly over the equator, so that in a geocentric universe, they do not follow a circular path with a center at the center of the earth, but follow a slightly smaller circle (offset from the center of the Earth) with a radius reduced by a factor of the cosine of the angular distance from the equator (that is, the astronomical declination). (This reduction by a factor of the cosine might be appreciated if one remembers that a star directly over the North pole of the earth does not make a large orbit of the earth, and that the cosine of 90° = 0. And note that the declination of a planet or other object in the solar system is variable and must be calculated or observed anew at each time.)

The Voyager 2 spacecraft had its closest encounter with Neptune August 25, 1989. At that time, Neptune was at a distance of 4,426,000,000 kilometers from Earth and was at (right ascension 18.716290 hours to 18.715309, difference=0.000981) declination -22.16°. Converting the distance to units based on the speed of light (299,792.458 kilometers/second), that is 14,764 light seconds = 4.1 light hours. That is to say, there was a delay of 4.1 hours for the signal from Voyager 2 to reach the earth. Assuming that Neptune and Voyager 2 were rotating daily around the earth, they were traveling in a circle of radius 4.1xcosine(-22.16)=3.8 light hours, and a circumference of 2π3.8 = 23.9 light hours in 23.93447 hours, or .999 times the speed of light. Not quite faster than the speed of light. But still, just how were those rocket scientists able to manufacture something that could approach the speed of light?

The Voyager 1 did not visit Neptune or other sufficiently distant object, but it is the most distant space probe, and is still sending information by radio. Recently it is at a distance from Earth of about 16,976,000,000 kilometers = 56,587 light seconds = 15.72 light hours. It is at right ascension 17.125 hours, rate of change unavailable but assumed to be negligible, declination 12.45°. Assuming that it is rotating daily around the earth, it is traveling through a circle of circumference 2π15.72xcos(12.45)=95.94 light hours in 23.93447 hours, or nearly 4 times the speed of light.

Of course, this is with the assumption that the Voyagers actually are exploring the solar system, and that we can trust the information about them from NASA. One might as well believe that the Apollo astronauts landed on the Moon. If one wants to avoid reliance on NASA, one can get the desired result at the cost of assuming the reliability of Earth-based measurements of the scale of the solar system and of the speed of light. At 0600 UT 2010 November 7, Neptune is at a distance of 4.4591x10^9 km from Earth at (stationary in right ascension 21.87855 hours) declination -13.39180°. That translates to 15313.92761 light seconds or 4.253868781 light hours, describing an Earth-centered circle of 2π4.253868781xcos(-13.39180)=25.94314203 light hours in 23.93447 hours at 1.083517425 the speed of light. One might be forgiven in wondering what force there is that accelerates the planet Neptune beyond the speed of light as its geocentric orbit increases with the approach to the equator.

Eris is a "dwarf planet" which is more distant than Neptune and Pluto. Its location on 2010 November 6 is at 796.222 light minutes (=95.73724 Astronomical Units) from the Earth at right ascension 01.6527 to 01.6522, difference=0.0005, declination of -4°21'11.4". This results in a geocentric circle with circumference of 2π13.2704cos(-4°21'11.4") = 83.14 light hours and a geocentric speed of 3.47 times the speed of light.

{ | class="wikitable" !Object !date !distance (light hours) !declination (degrees) !change in right ascension (hours per day) !circle circumference !speed (speed of light) !Reference 23.9|0.994 }
 * + Geocentric values for solar system objects
 * Voyager 2 @ Neptune
 * 1989 Aug 25
 * 4.1|
 * 4.1|
 * Voyager 1| |15.72|12.45|95.94|4.0|
 * -|Neptune|2010 Sep 06|4.1299|-13.39183|25.24335 1.0518|
 * -|Eris|2010 Sep 06|13.2704|-4.3531|83.14|3.46|
 * -|Neptune|2010 Sep 06|4.1299|-13.39183|25.24335 1.0518|
 * -|Eris|2010 Sep 06|13.2704|-4.3531|83.14|3.46|

The distance in light hours is the distance in kilometers divided by the speed of light in kilometers per hour (299,792.458 kilometers per second divided by 3600 seconds per hour). The circle's radius is the distance times the cosine of the declination. The circle circumference is the radius times 2π. The (geocentric) speed is the circle's circumference divided by 23.93447 hours (that is, one sidereal day, the period of geocentric rotation, ignoring the small daily orbital motion in right ascension for objects beyond Uranus ( for which it is ~42"/day)).

mjd        Planet RA PlanetDec  earthdist 55506.25000 21.878874 -13.39181 4.4566E+09 55507.25000 21.878855 -13.39180 4.4591E+09 55508.25000 21.878874 -13.39160 4.4617E+09

Minimum distance to Venus 38.2x10^6km Mercury  77.3 Maximum distance to Venus 261.0x10^6km Mercury 221.9

1 Astronomical Unit = 149,597,870.691 km 1 light-hour = 1.0792528488 × 1012 m

Atomism
Atomism is an ancient belief in the West going back to Democritus, and famously expounded by Lucretius in his philosophical poem De rerum natura ("On the Nature of Things"). The word "atom" in Greek means "not-divisible". The philosophical atomists believed that all things ultimately consisted of smallest, indivisible particles. Part of this belief was that all things were material, and thus the atomists were materialists, and, by implication, atheists (although they might believe in material gods, this was little solace to proper theists). The atomists were practically the only materialists or atheists of philosophical note in the Western world through the Middle Ages, and atomism was considered to be synonymous with (rather than just one variety of) atheism. One of the features of atomism was that the atoms moved randomly, and combined at random to form various things, with only those things which were viable surviving. Thus they have been thought of as precursors to the theory of natural selection. Indeed, many of the old arguments against atomism have been retreaded to be arguments against evolution, no matter how poor the fit. Despite the long history of opposition with religion, there seem to be no surviving anti-atomists, not to the extent that there are anti-evolutionists and even anti-heliocentrists. One might imagine that philosophical anti-atomists would have been encouraged by the discovery of the splitting of the atom, but one must be wary of ascribing too much rationality to crackpots.

Deep homology
A deep homology is a homology which spans a wide stretch of the tree of life, often not apparent except through study of the proteins or genes involved. One such example is the deep homology between the cluster of genes responsible for the building of blood vessels in vertebrates and in a yeast, for fixing cell walls.

Deep homologies are evidence of common ancestry across wide ranges of the tree of life. Furthermore, they are indications of how "irreducibly complex" structures can evolve new functions from precursor structures. And certain cases suggest research programs into problems of medicine (in the vertebrate-yeast case, for the treatment of cancer).

=How do you know, were you there?= Several young earth creationists don't think that we can know anything, except by direct, personal observation, and have even encouraged kids to challenge their science teachers by asking, "How do you know, were you there?". Creationists are fond of sound bites, when to take a question seriously it often requires a longer attention span. But let's try, anyway, to treat this issue with as brief responses as serious treatment can abide. == =You can't prove a negative= You can't prove a negative is a saying of philosophical folklore. One of those things that "everybody knows", but which is happens to be wrong.

Mathematicians and logicians are quite familiar with proofs of negatives. Indeed some of the major developments of mathematics ever since the ancients have been proofs of negatives:
 * There is no rational square root of 2.
 * There is no largest prime number.
 * The WP: Seven Bridges of Königsberg problem has no solution.
 * There is no method for solving the general fifth-degree polynomial using addition, subtraction, multiplication, division, and extraction of roots.
 * There is no general way of trisecting an angle using compass and straightedge.
 * There is no proof of the "WP:Parallel postulate" in geometry from the other postulates.
 * Gödel's incompleteness theorems are proofs of negative statements, that one can't prove certain things in certain systems.

Insofar as "proof" has any meaning at all with respect to non-formal systems, one can establish with as much certainty as desired certain negative propositions. If you can't "prove" negative statements like these, then you can't prove any positive statements, either:
 * There is no twenty-mile high mountain on earth.
 * There are no invertebrate mammals.
 * There is no second natural moon of the earth which is visible to the naked eye.

As it turns out, the very claim that you can't prove a negative is self-defeating, for "you can't prove a negative" is a negative statement. So how can you expect to be able to prove that? Why should we believe it? Do you just expect us to take your word for it?

=Adaptive immune system= The adaptive immune system, a signature trait of the jawed vertebrates, is an enhancement of the immune system. It has relevance to the "controversy" over creationism/intelligent design versus evolutionary biology in more than one way. The adaptive immune system has been one of the more frequently used examples of features of the world of life which could not have evolved, and therefore (tacitly assuming that there is no other alternative) must have been intelligently designed. This article examines the "strengths and weaknesses" of using the adaptive immune system in an argument for intelligent design.

The adaptive immune system builds on the more widespread innate immune system (which occurs not only in invertebrate animals but also plants and elsewhere) by generating defenses against alien bodies which are new to the animal, even those which do not exist in nature. The innate immune system serves as a defense against a limited (albeit large) range of potential threats. But the adaptive immune system serves as a defense against the evolution of disease-causing organisms, as well as organisms which are otherwise new to the protected animal. It is the adaptive immune system which is activated by vaccination.

The system works by generating random variations in the defense mechanism against foreign bodies. When a particular variation does not work, that variation is not repeated. When a particular variation happens to work (and there is no "choosing" of that variation: the body does not "know" in advance what will work), then that variation is preferentially generated to eliminate the foreign body. For the technical details see the Wikipedia article WP:Adaptive immune system.

Irreducible complexity
The adaptive immune system was among the few examples first proposed to indicate that "irreducible complexity" was evidence that something could not have evolved. Thus it is an exemplary test case, one proposed by the anti-evolutionists, for the reliability of that methodology. For if a methodology can be shown to reach a false conclusion, then that tends to case doubt on the methodology. Especially so when the false conclusion is reached in an example proposed by the advocates of that methodology. Either the premises for this particular application of the methodology were not true, or the conclusion actually is true, or the methodology was not correctly applied, or else the methodology is not reliable.

As the conclusion of the "irreducible complexity" argument with respect to the adaptive immune system is that it is impossible for the system to evolve, the conclusion is falsified merely by demonstrating that it is possible for the system to evolve. It is not necessary to demonstrate the far stronger statement that a particular sequence of events took place in the evolution of the system. A demonstration that there is at least one evolutionary scenario which is consistent with irreducible complexity but not intelligent design is sufficient to call into question the methodology of the argument from irreducible complexity. To be sure, it is more satisfying to have a sequence that is plausible or (better yet) even likely.

The adaptive immune system serves as a counter-example to the correctness of arguing from irreducible complexity to intelligent design.

Because it is possible for the adaptive immune system to evolve, and, beyond that, it is even likely that it has evolved, the existence of the adaptive immune system causes problems for the methodology of irreducible complexity.

Random variation and selection
The adaptive immune system is effective because it operates by the generation of "random" (that is, not directed towards a particular goal) variations and "natural" (thatxxxxxxxxxxxxxxxxxxxx is, no supernatural action is required) selection. Thus it is a model of a natural biological system which produces a result without "intelligence" or "design" which can be observed operating predictably, repeatedly, in real time. Therefore it presents a test for any argument against evolution which says that random variation and natural selection cannot produce an effect. Again, the soundness of the argument presented against the efficacy of "random variations and natural selection" is presented with a test, and the fact that it fails to agree with the operation of the adaptive immune system suggests that the methodology of that argument is not reliable.

The adaptive immune system serves as an example of how random variations and natural selection can be productive.

Conflict in the world of life
The adaptive immune system operates only in a world where one biological system (the animal that has the adaptive immune system) is in conflict with another biological system (the disease agent infecting the animal). If both biological systems are "intelligently designed", then it sheds some light on the nature of ID, specifically that one design can make sense only by its being in conflict with another design. The bacterial flagellum serves the bacterium by making it more effective infectious agent in jawed vertebrates, and the adaptive immune system serves the jawed vertebrate by making it more resistent to bacteria. If the designer didn't want bacteria to cause diseases, could not they have been designed without flagella?

The adaptive immune system serves as an example of a difficulty for the existence of a single design.

The tree of life
The adaptive immune system is characteristic of the Gnathostomes, or jawed vertebrates, that is, most familiar forms of fish (cartilage or bony fish), reptiles, mammals and birds, which is consistent with the idea that it is a feature which originated in that branch of the tree of life and is an evolved feature which is preserved in that lineage only because, despite its complexities, it is preserved by natural selection. There is no known other explanation for why it is restricted to jawed vertebrates - having a skeleton with jaws does not seem to call for a design of the immune system, nor does lacking jaws seem to compensate for not having an adaptive immune system. Why would a designer give the same kind of immune system to sharks and humans, but not to octopuses or butterflies?

The adaptive immune system serves as an example for common descent with modification.

Sudden appearance?
Consider a scenario in which the early jawed vertebrates were without an adaptive immune system, and then suddenly they were endowed with the full-blown adaptive immune system (by assumption, it was not gradually introduced). This was a major innovation which overnight transformed animals which managed to survive into what must have resulted in a tremendous comparative advantage over other animals (not to mention over the infectious agents). How did those other animals manage to survive in competition with the many species of newly advantaged jawed vertebrates? Compared to this, the introduction today of a single new invasive species is an extremely minor event.

The adaptive immune system serves as an example of a lack in "sudden appearance".

Failures in immunity
As elsewhere in the world of life, the adaptive immune system has its problems, both by its failure to operate when it could protect, and by its operating in ways that harm rather than protect.

Severe Combined Immune Deficiency
A genetic variation causes what is essentially a total failure of the adaptive immune system in newborns. SCIDS is informally known as the "bubble boy" syndrome, after the famous case of "David", a boy who survived to the age of 12 only by keeping him isolated inside a barrier protecting him from all of the pathogens in the outside world.

In a study of treatment of the syndrome, "nondefective copies of an ADA gene were transferred ... into each of 10 young children with SCID. ... all 10 children who received the transgene survived the trial periods (which had a median of four years); and, importantly, their immune systems appeared to have been substantially restored by the gene therapy." "Suffice it to state the following: to ascribe flaws in the human genome to insuperable technical hurdles for the Intelligent Designer could be taken to imply that a benevolent Creator God was even more challenged, technologically, than are we mere humans ..."

Allergies, autoimmune diseases, anaphylactic shock, asthma
In a variety of cases, the adaptive immune system is active in such a way as not to protect against disease-causing organisms, but to cause distress. For example, common allegies can be a result of the immune system reacting against environmental factors which present no threat; and autoimmune diseases are a result of the immune system reacting against the body's own cells. These failures can range from a mild irritation to life-threatening illnesses.

No known design can produce this feature
Some times a creationist gets carried away in describing the wonders of life, and brings up the point that this particular wonder is so wonderful, so beyond comprehension in its complexity, that no scientists have managed to design anything approaching it. Because this wonder is so unlike what we know as design, well, then we are supposed to conclude that it is designed. Really, because it is so unlike design, therefore it must be designed?