Intelligent design

Intelligent design (ID) is the claim that fundamental features of the universe and living things are best explained by purposeful causation—a "higher intelligence." Proponents of ID argue that conventional biological theory of evolution through natural selection cannot explain the origin of many highly complex features of living organisms; they argue that some such features are better explained as the result of the intervention of a directed process that they describe as an intelligence. Critics of ID consider that these arguments are logically unsound and reflect a flawed understanding of modern biology; they believe that conventional biological theories explain the evolution of complex features of organisms elegantly and efficiently. Critics have also accused its supporters, nearly all of whom believe in a personal God, of using ID primarily as a way to get around U.S. legal restrictions on teaching about God in the classroom. However, ID proponents claim that ID does not require belief in a personal God to support its arguments.

The U.S. National Academy of Sciences has concluded that, in its present form, ID cannot be regarded as scientific because the claims made by its proponents are not testable. See intelligent design movement for an account of political efforts to promote education about ID in schools.

Arguments for intelligent design

The classic design argument for the existence of an intelligent creator may be traced from ancient philosophy, through the works of medieval scholastics such as the philosopher-theologian Saint Thomas Aquinas (1225-1274), who argued that the existence of God could be deduced by reason.

In the 18th century, the theologian William Paley (1743-1805) introduced the "watchmaker analogy", one of the best known metaphors in the philosophy of science, as an argument for the existence of God. The argument is, in essence, as follows: Imagine walking on a pebbled beach, where the pebbles may be wonderfully shaped, beautiful in different ways, interesting and varied one from another. However interesting and beautiful you find them, you will not doubt that they are the products of purely natural causes. However, if amongst the pebbles you find a watch, even if you have never seen a watch before, you will immediately recognise it as qualitatively different from the pebbles. Inspecting it, from the intricacy of its design, and the clear purpose of that design, you will inevitably and correctly conclude that the watch is not a 'natural' object but an artifact, something designed by a powerful and intelligent agent.

Casual observation might similarly lead to the conclusion that, compared to a watch, even the simplest living form is incredibly complex, giving it the appearance of being designed for a purpose. There must be a designer, said Paley, "and that designer is God."

To many who believe in a Creator of the universe, the idea that the nature of living things might contain some evidence that they have been built purposefully rather than having been evolved by natural selection is a natural one. Some modern proponents of ID have accordingly broached this issue in a theoretical manner, by considering how, objectively, it might be possible to ascertain whether any particular object has been designed for a purpose as opposed to having evolved to fit an apparent purpose. Thus, William Dembski has argued that ID can be formulated as a scientific theory of information that has empirical consequences and which is devoid of any religious commitments.[1] By this view, intelligent design asks whether design can be detected in nature from purely scientific and mathematical considerations.

These proponents have proposed two criteria for deciding whether something has been designed in a way that cannot be accounted for by evolution through natural selection:

Irreducible complexity

The first criterion relates to the notion of "irreducible complexity". Proponents of ID argue that irreducible complexity is a common feature of biological systems, and claim that it cannot plausibly be accounted for by evolution through 'undirected' natural selection. They argue instead that irreducibly complex systems must have arisen by some form of 'directed' evolution, i.e. towards a predetermined end.

A complex system is a system with many component parts, and which depends on many interactions between those component parts to perform its particular defined function. A system is irreducibly complex if removing of any one of these parts causes it to cease functioning. In No Free Lunch, William Dembski extends this basic definition, and states that a system is irreducibly complex

"if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function."

Intelligent design components claim that when the final form of a structure requires the involvement of each of several different elements for the final form to have any effective functionality, it would be impossible for this structure to have evolved, and would thus be evidence for creation. However, duplication of genes, followed by differentiation, can cause one (for example) protein that fulfilled two roles to now have two genes coding for it. If each of these genes evolves to specialise in a different aspect of the original function, followed by further duplication, it is possible for an irreducibly complex web of highly specialised proteins to emerge where one protein fulfilled the role eventually. Indeed, if this duplication and specialisation allows the new pair of proteins to fulfil the role better than the original - which is not unlikely, given the tradeoffs of a single, generalised protein - then natural selection will select for irreducible complexity.

Specified complexity

Intelligent Design advocate William Dembski advances the concept of specified complexity or complex specified information as describing in a theoretically rigorous way the procedure used to identify objects which have been designed. The argument is deductive. Designed objects are those objects which cannot be explained through hypothesis of chance or natural law - the so-called Explanatory Filter (EF). What Dembski proposes in the idea of CSI/SC is quite different from other analytical accounts of information. It is not information in the sense used by Claude Shannon and Warren Weaver, nor is it complexity in the sense used by Andrey Kolmogorov.

The second criterion relates to the concept of "specified complexity". Complex structures can arise by natural processes, or by chance mechanisms and some may happen to have functionality that can be exploited; thus complexity per se is not evidence of intentional design, nor is the improbability of a structure or pattern arising by simple chance any evidence that it did not in fact arise by chance. However, proponents of ID argue that when a structure clearly fulfils a function that is essential for the function of living things - in other words when an outcome of an evolutionary process is absolutely required by the organism, then they argue that it is legitimate to consider how likely it is that that outcome could have been achieved through the chance processes that are said to be involved.

Dembski's proposed technique of calculating specified complexity has never been applied, by him or anyone else, to any structure or function in any biological system.

Modern Evolutionary Synthesis

ID proponents argue that the natural selection mechanisms that have been used to explain the "apparent design" of numerous components and interactions of living organisms cannot explain all features of organism complexity, but their critics argue that they underestimate the sophistication of modern evolutionary theory, and in particular underestimate the creative capacity of natural selection.

The currently accepted account of the origin of living things is known as the "Modern Evolutionary Synthesis". This expresses the theory of evolution by natural selection in a form consistent with molecular biology and population genetics. By this theory, all extant living things are the products of descent with modification from common ancestors that lived 3-4 billion years ago. This theory (and an abundant array of evidence of evolutionary process that are seen in nature) explains all evolution as resulting from processes of natural selection among populations among which genetic novelty and novel combinations of genetic components are generated by many different genetic mechanisms. Natural selection is not the single simplistic process that the common characterisation "survival of the fittest" suggests, but embraces a very wide array of processes and pressures that lead to differential reproductive success in populations. The creative elements of natural selection emerge because, as selected genotypes accumulate over many, many generations and combine in different ways to produce novel phenotypes, this produces a huge diversity of organisms (today there are more than 10 million living species, a tiny percentage of all the species that ever existed).

There are important features that distinguish the 'design' achieved by natural selection from the kind produced by an intelligent designer. Natural selection is undirected in that it has no preordained plan, but is simply a result of the differential survival and reproduction of living beings. Natural selection and genetic mechanism provide powerful ways of generating novel features which are stored in the DNA code and passed on to the subsequent generations, but natural selection has no foresight, and so environmental changes may threaten the survival of organisms that were thriving. As a result, species extinction is common: it is estimated that, of all the species that ever lived on Earth, more than 99% are now extinct. Critics of ID see the evidence of massive extinction of species as inconsistent with the notion of intelligent design of the world we live in.

Although most descriptions of evolution assume that all mutations are random with respect to their effects on fitness, some biologists argue that there are important mechanisms which make favourable mutations more likely to occur. For example, Lynne Caparole has argued that natural selection favours some mechanisms that increase the likelihood of mutations in particular genes. These mechanisms produce considerable diversity in gene function amongst progeny, and this diversity can facilitate rapid evolution.

In particular, not all mutations rely on a random change to a single nucleotide base: some involve "mis-copying" the DNA, and these errors are very common for certain types of DNA sequence. For example, when a section of DNA contains a short repeated sequence of nucleotides, the number of repeats can be affected by a common "stuttering error" in DNA replication. The consequences will depend on exactly where in the genome the repeated sequence is located, but if, for example, it occurs in a region that affects how a bacterium responds to an antibiotic, then this diversity makes it more likely that some offspring will be antibiotic resistant. Thus, although accuracy is generally very important in reproducing a genome, some 'errors' are valuable, because the increased diversity of the offspring makes it more likely that some will be well fit to rapidly changing environmental conditions.

ID publications

Many books on ID have been written but few ID research papers or monographs have been published in conventional peer-reviewed scientific journals. However, ID advocates have created several journals devoted to publishing papers on ID (see Bibliography). The Kitzmiller vs Dover Area School case in 2005 was the first direct challenge brought in U.S. federal courts against a public school district that required ID to be presented to students as an alternative to evolution as an explanation of the origin of life. The plaintiffs successfully argued that ID is a form of creationism, and that the school board policy therefore violated the Establishment Clause of the First Amendment to the Constitution. In testimony, ID proponent Michael Behe admitted that “There are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred.”

On 4 August 2004, a review article by Stephen Meyer, an ID proponent, appeared in the peer-reviewed Proceedings of the Biological Society of Washington, questioning conventional evolutionary explanations for the Cambrian Explosion and proposing ID as an alternative The review questions whether whether conventional biological theory can explain the information explosion evident during the Cambrian period. He says: "For neo-Darwinism, new functional genes either arise from non-coding sections in the genome or from preexisting genes. " He argues that the first leaves too much to luck and chance to be plausible, and the second has the problem that changes to existing genes are almost invariably deleterious. However this neglects many conventional accounts of how genes evolve, including probably the major known mechanism whereby novel genes arise, via gene duplication. Gene duplication is very common through evolution, and means that one copy of a gene can continue to sustain its normal function while the other is "surplus", and is free to accumulate mutations. Thus, by conventional explanations, a new gene doesn't have to be built from nothing - instead evolution is handed an already functional "toy" to play with.

Later, the Council of the Biological Society of Washington retracted the article. The managing editor for the journal at the time, the process structuralist Richard Sternberg, stated that the article had been properly peer reviewed by three well qualified referees. His decision to publish the paper nevertheless resulted in protests, and colleagues at the Smithsonian Institute, where he was employed, sought to discredit him and created what the The U.S. Office of Special Council (which is authorized to investigate allegations of prohibited personnel practices and activities prohibited by civil service law) called "a hostile working environment".

The lack of peer-reviewed articles is cited by some as evidence that ID is unscientific. ID supporters point to the Proceedings incident as showing the opposite: that the scientific climate is so prejudiced against ID that not even peer review is enough to overcome publication bias. ID proponent Dominque Tassot of the 'Center for Studies and Prospectives on Science', France, states the reasons as

"[Evolutionary scientists] live and think inside the paradigm of evolution. As Thomas Kuhn explained [in The Structure of Scientific Revolutions], theories are accepted or rejected in order to defend the dominant paradigm. Information which conflicts with that paradigm is set aside, it doesn’t get published."

Is intelligent design a form of creationism?

Most proponents of ID are also creationists, meaning they believe the universe was created by a deity or some other power beyond the full comprehension of mortal man. The hypothesis, however, is not the same as young earth creationism, which is a belief that the account of the creation of the universe and of life as given by the Bible is literally true. ID does not try to identify the designer as supernatural, nor does it try to establish the veracity of a particular narrative, although some leading proponents have stated that they believe the designer to be the Christian God. However, some proponents of ID see no conflict between it and evolution, and indeed see evolution as evidence of ID. Many proponents avoid any personification of the source of the ID, and so the focus of ID is different to that of arguments in natural theology, such as the teleological argument.

Criticisms of intelligent design

Proponents of ID argue that it is a scientific theory rather than a matter of religious belief, despite its base of support in the religious community. Courts in the USA have rejected this argument, in part because, for a theory to be 'scientific', it must generate predictions by which it can be tested; in other words, it must be open to attempted disproof.

Critics also hold that the postulate of an intelligent designer is not an explanation for life at all, but a "deus ex machina"--that is, an evasion of attempted explanation. They consider that ID is not a serious alternative to modern biological theory, in particular they consider that the complexity of biological systems can be well explained by conventional biological theory. They also consider that the tenet of ID that perfection in design needs a directing intelligence is inconsistent with many examples in nature of imperfections in design of organisms.

There are also many critics of ID who are religious, and who believe that the role of science is to seek natural, physical explanations of the world; although they believe that there is a God who created the world and life in it, for them this is a matter of faith not of science. Some critics doubt the intellectual honesty of ID theory, in that they consider that the only reason for promoting it is for the religious message that it implies, not for the intrinsic merits of the arguments.

While some proponents of ID see evidence of design in how well complex structures fit their purpose, molecular biologists see something very different in the fine details of those structures. So far from seeing genetic information being perfectly and economically fashioned to suit a given purpose, they see wastefulness, duplication, errors, and the detritus of now redundant genes in gene sequences — in other words, things they would expect to see as the residue of evolution by natural selection. In short, despite the appearance of efficient design at a high level, at a molecular level the design shows few signs of purposeful intelligence but many signs of chance processes. However, other proponents of ID note that ID does not imply perfection in design; after all, of the things that we know to be the result of intelligent design — things designed by people — few are perfect.

Conventional explanations for the origins of irreducible complexity

By the original common and uncontroversial definition, many biological systems are irreducibly complex. However, conventional evolutionary theory has no intrinsic difficulty in explaining how a system can have arisen by natural selection and yet appear to be irreducibly complex.

The key assumption which is problematic for ID is the assumption introduced by Dembski that the 'basic' function of a system is the same as its 'original' function. Biologists argue that, on the contrary, systems often evolved for one purpose and then were "exapted" to a different function. An example is the evolution of the wing: a small wing is useless for flying, so how could an aerodynamically effective wing ever have begun to evolve? However, even small wings can be used to increase running speed. The aerodynamic properties of the wings would have been incidental to the original function, but once a species had evolved wings that were big enough for gliding, then this (originally incidental) benefit may have become the major focus of subsequent natural selection.

Another way by which a system might become irreducibly complex is via the eliminative actions of natural selection. For example, genes that were once important in precursor forms of an organism are likely to be eliminated by natural selection if they later become redundant. Many see this as analogous to the scaffolding and buttresses that are used to construct a building, which are then removed after the building is completed, thereby eliminating all evidence of exactly how the building was built. Thus, in a currently living organism we see only the final structure, with little remaining evidence of the "scaffolds" by which evolution built it.

Michael Behe further adapted Dembski's definition to apply it to evolutionary pathways:

"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations)."

This step makes an overt link between irreducible complexity and ID. As a definition, it can only be applied after assuming that evolution was directed (i.e. after assuming that there is any such thing as an unselected mutation)

Conventional explanations for rapid evolution of complex traits

ID proponents doubt that known genetic mechanisms can explain how organism evolve rapidly to achieve complex design outcomes, given that evolution requires rare mutations to arise through chance processes.

According to conventional biological theory, spontaneous mutations are the ultimate source of genetic novelty. One of the first estimates of the rate of spontaneous mutation in humans was made in 1930 by JBS Haldane ; his estimate, which was very close to the current best estimates, was that every new human baby that is born has 100-200 novel gene mutations. Thus, in every generation, vast numbers of new mutations arise within a population; most are neutral, but a few are beneficial. However, for any beneficial mutation to become fixed in a population takes many generations. In 1957, Haldane estimated that, for a population of stable size, it takes about 300 generations for a new mutation to become fixed in a population. This conclusion was independent of the strength of selection pressure unless it is very intense, explaining the slowness of evolution by natural selection.

Accordingly, ID proponents have questioned, for example, whether there is enough time since the last common ancestor of humans and chimpanzees to explain the genetic differences between them.

This is not an argument that can be easily dismissed. Evolution does not proceed serially, by fixing first one genetic change and then the next, but in parallel: selection pressures apply simultaneously to all mutations that arise. It is not at all clear how quickly evolution by natural selection can occur when several traits are being selected for simultaneously, but Haldane warned that it could be very slow. However, he noted that evolution can occur much more rapidly when environmental pressures are changing. The last 10 million years has seen dramatic global changes in climate, and any species, over such a timescale, will encounter many other changes in selection pressure through the ever-changing ecological balance.

Modern genetics has identified many mechanisms that enable some organisms to evolve rapidly in a quasi-directed fashion In multicellular organisms, sexual selection is one of these, and Mobile DNAs are another (See DNA and molecular evolution.) The human immune system is a good illustration of such mechanisms. The creation of highly adapted antibodies that neutralise poisons and pathogens to which the body has never been exposed before, occurs by such natural selection events in rapidly evolving cells of the immune system (see Clonal Selection Theory of Acquired Immunity). Conversely,pathogens use equally powerful genetic strategies (such as sets of alternative genes for related structures) to evolve rapidly and to deftly switch their antigenic features so as to evade the immune system.

Could the flagellum have evolved by natural selection?

Many ID arguments are based on the notion that every piece of a biological machine must be assembled in its final form before anything useful can emerge.

For example, the flagellum is a complex structure that allows bacteria to move; up to 40 different proteins must be arranged in a very particular way for the flagellum to work. Proponents of ID argue that a flagellum is useless if it won't move, that it needs all of its parts to function, and that it is hard to conceive that it could have arisen by classical natural selection. Natural selection involves gradual cumulative mutations, each of which produces a gain in fitness; the ID argument is that the flagellum has adaptive value only when fully assembled - the intermediates are useless.

To biologists generally, this idea is a misconception. Evolution by natural selection produces complex biochemical machines by copying, modifying, and combining proteins that were previously used for other functions. Evolutionary theorists argue that many features of organisms evolved to fit one function and were then adapted through natural selection to fulfill a different function. By this view, natural selection is not a single path, but a multiply branching path with many dead ends, with many branching points where genes were duplicated, and with many changes of direction where the 'destination' changed.

Flagella are modular devices and the modules serve other functions

Flagella are modular devices, that exist in thousands, if not millions of versions in nature. Many radically different variations of flagella design occur, some rotate in two directions, others only in one. However, there is evidence that the flagellum structure arose from structurally simpler structures by gene duplication and further evolution. It appears that the flagellum proteins evolved from just two precursors (a proto-flagellin and a proto-rod/hook protein) by several rounds of gene duplication and diversification.

Many of the versions of flagella lack many of the particular components that, in other versions, seem to be irreplaceable. For example, in Gram positive bacteria the P- and L-rings present in the flagella of Gram negative bacteria are missing.

Relatives of some flagellum proteins are used in other bacterial structures. A protein similar to flagellum component FlgA is used in assembly of Type IV pili surface appendages; these are superficially like flagella, but have no major role in movement. Flagellum protein FlgJ contains a region that digests the rigid bacterial cell wall during flagellum insertion through the wall, and many similar bacterial proteins do other tasks.

All flagella include modular subcomponents called T3SS that are widely used by bacteria for secretion of proteins. This T3SS submodule is used to assemble the flagella, but is also used to secrete other molecules from the cell. There are also versions of flagella that are defective in providing motility, but which have a functional role in infection (e.g. in the pathogen Brucella melitensis)- evidence that components of flagella have useful biological functions apart from movement.

The modularity of flagella is not unusual in complex biological structures. Bacteria possess a wide variety of complex structures such as pili, secretion systems, and conjugation machinery. As a (richly documented) general rule, any particular module may have several different roles (in for example, secretion, uptake, protein of DNA injection or twitching motility) and complex structures are built by "mixing and matching" different sub-components. This general rule provides evolutionary explanations of biodiversity.

In summary, many components of the flagellum are used by bacteria for other functions, such as for injecting poisons into other cells, and these components are not irreducibly complex in these other functions. Accordingly, biologists think that different elements of the flagellum evolved separately to fulfill other functions in ancestral organisms. They thus think that motility arose relatively late in bacterial evolution, after many of the elements used in the flagellum had already evolved.