Put a Sock in It

{{Creationism}}
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"'''Put a Sock In It'''" is a rambling screed on [[William Dembski]]'s blog ''[[Uncommon Descent]]''.<ref>[www.uncommondescent.com "Put a Sock In It"], ''Uncommon Descent''</ref> In it, he presents the following "comment" policy — a list of arguments that evolutionists are not allowed to make because they are "settled." Given here in an abridged form, it is a series of [[straw man]] arguments, avoiding the real fallacies of [[intelligent design]].

Put a sock in it yourself, Dembski!

{{sbs|title=1|Dembski's text|RationalWiki's responses}}

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<h3>Arguments we’ve heard many times before and don’t want to hear again.</h3>
If you insist on boring us with them you won’t be with us for long.

...

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<h3>Introduction</h3>
How about things that ''we'' don't want to hear [[ad nauseam|''yet again'']]; that the Grand Canyon is evidence of a [[global flood]], [[macroevolution]] can't happen, [[mutation]]s can't be beneficial, evolution has never been observed, how do unconscious atoms gain consciousness ... you know, [[PRATT|the usual tripe]].
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<h3>Who Designed the Designer</h3>
This argument points out that, by inferring a designer from complexity in machines, the designer must also be complexity. Why? Well just because it seems like he/she/it would. This of course then plunges into an infinite loop of who designed the designer. This infinite loop makes Intelligent Design somehow impossible. The really weird part is the argument is broadcast to us using a computer that was the result of intelligent design. Intelligent design does not speak to the nature of designers any more than Darwin’s theory speaks to the origin of matter.

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<h3>Who is the designer, anyway?</h3>
Dembski attempts to answer a salient objection to intelligent design: if complex things, like '''intelligence''', require a designer, what designed the designer? He then attempts to handwave away this question in puzzling ways. First, by implying that the designer may not be complex, Dembski leaves a simple, undesigned designer developing the universe. This sounds very close to evolution, and ''not'' like Intelligent Design (would you say God, for instance, is a ''simple'' being?). His second point, about questioning intelligent design when working with designed machines, is irrelevant to the case of intelligent design as machines are not (yet) self-replicating organisms. Finally, by attempting to equate the designer to abiogenesis, Dembski fails for a third time. Evolution specifically deals only with living organisms, and is thus limited in scope to living things. Intelligent design is supposed to apply to everything, giving us a tool to determine if something has been designed or not. However, their designer gives every indication of being itself designed.
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<h3>Intelligent Design is Creationism in a Cheap Tuxedo</h3>
No, it isn’t. Are you capable of comprehending the concept that a theory being consistent with a philosophical, religious, or metaphysical belief as distinct from being the belief itself or being founded on that belief? ID is consistent with religion but is not itself a religion nor is it founded on religion. ID is also consistent with non-religious beliefs like panspermia. Creationism is an attempt to take the biblical account in Genesis and find scientific evidence of it. Religious groups are always likely to be involved to a certain extent since ID gives epistemic support in the form of greater explanatory power for their theology.

Intelligent Design is no more and no less than detecting patterns that can be independently given and whose probability of occurring by chance interplay of matter and energy are too improbable to be reasonable. It is meeting the challenge in Darwin’s Origin of Species that if any structure in a living creature cannot be constructed by small steps, where the structure at each step is useful to the creature, then it falsifies the theory of natural selection. ID is a modern scientific offshoot of philosophic arguments from design such as Aristotle’s first cause and Paley’s watchmaker, which predate unconstitutional creation science by thousands and hundreds of years respectively. The only cheap thing in this is that it’s a cheap shot to censor a valid scientific hypothesis by conflating it with religion that a court will find violates the establishment clause of the First Amendment.

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<h3>Creationism, I think so!</h3>
But the term "[[intelligent design]]" only came to be widely used after creation science had been banned from US public school curricula. Coincidence? Nope. The links between the creationism and intelligent design movements are well documented (see: [[cdesign proponentsists]]). The artificial division between the two concepts is a major part of the ID movement's [[wedge strategy]] to get intelligent design taught in schools.

Concepts like [[directed panspermia|panspermia]], the idea that life originated outside Earth but arrived here either deliberately or accidentally (such as on meteorites), which was theorized by scientists a few decades ago but is now rarely suggested, are often referenced by intelligent design proponents. In fact such ideas rely on different arguments and forms of evidence than those used by the ID movement, and do not necessarily imply a "designer". Panspermia also only explains '''life on Earth''' and not life in the universe, which, by the fact that life would have to have arisen somewhere, still leaves ID an unlikely answer.

Scientific research in which "religious groups are always likely to be involved" is not apt to make for an objective application of the [[scientific method]], because religious groups tend to actively discourage questioning their presuppositions, which is something absolutely essential to the scientific method.
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<h3>Since Intelligent Design Proponents Believe in a “Designer” or “Creator” They Can Be Called “Creationists”</h3>

By that measure Darwin was a Creationist and the Theory of Evolution a Creationist theory:

{{quotebox|There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved. –Charles Darwin}}

Anyone who thinks a design inference is warranted is in some sense a “creationist”. The argument hinges on conflating “creationist” with biblical creationist. One can be the former without being the latter. ID proponents may also believe in God, a Creator, Genesis, or they may be agnostic. However, ID is the effort to form scientific theories based on empirical evidence, rather than on religious texts (whether true or not).

In principle many ID proponents would not mind being labeled as a “creationist” in a general sense. The problem is that it causes confusion since it doesn’t recognize the significant distinctions. Mankind has always been interested in investigating the relationship between God and nature. At times, philosophy defined the debate; at other times, science seemed to have the upper hand. What has always mattered in this discussion is in which DIRECTION the investigation proceeds. Does it move forward? That is, does it assume something about God and then interpret nature in that context. Or does it move backward? That is, does it observe something interesting in nature and then speculate about how that might have come to be? If the investigation moves forward, as does Creationism, it is faith based. If it moves backward, as does ID, it is empirically based.

Each approach has a pedigree that goes back over two thousand years. We notice the forward approach in Tertullian, Augustine, Bonaventure, and Anselm. Augustine described it best with the phrase, “faith seeking understanding.” With these thinkers, the investigation was faith based. By contrast, we discover the “backward” orientation in Aristotle, Aquinas, Paley, and others. Aristotle’s argument, which begins with “motion in nature” and reasons BACK to a “prime mover,” is obviously empirically based.

To say then, that Tertullian, Augustine, Anselm (Creationism) is similar to Aristotle, Aquinas, Paley (ID) is equivalent to saying forward equals backward. It has nothing to do with subjective interpretation.

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<h3>Splitting hairs, are we?</h3>

''Translation:'' Don't call us creationist, because then we'll lose court cases and can't proselytize your kids.
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<h3>Intelligent Design is an Attempt by the Religious Right to Establish a Theocracy</h3>
Hyperbolic nonsense. As valid as saying Darwinian evolution is an attempt by the atheist left to eliminate religion. Now some ID proponents may assert that people don’t WANT Darwin to be wrong, they simply don’t WANT there to be a designer of any type, because that threatens their worldview.

There is some truth to this statement, but only to a certain extent. For example, Richard Lewontin, the eminent author and Professor of Biology at Harvard from 1998 through 2003, is famous for his quotes. He states “We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world , but on the contrary, that we are forced by our a priori adherence to material causes….Moreover, materialism is absolute, for we cannot allow a Divine Foot in the door.”

But to be fair, Darwinists are a diverse bunch and many are religious. BUT they have their own personal philosophical views on their own religion that they believe conflicts with design (like “God would not have done it that way”).

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<h3>Ever hear of the [[Wedge Document]]?</h3>
To quote Wikipedia's "Wedge strategy" page, "The Wedge strategy is a political and social action plan authored by the Discovery Institute, the hub of the intelligent design movement."<ref>"Wedge Strategy". ''Wikipedia''. January 16, 2009. http://en.wikipedia.org/w/index.php?title=Wedge_strategy&oldid=264584089.</ref> While it may not be the "mainstream" religious right that props up the ID movement, it is clearly conservative and clearly based in religion (although "theocracy" is clearly overstepping rational argument).

In fact, Dembski doesn't address the alleged fallacy at all: he just handwaves it away as "hyperbolic nonsense" before waffling irrelevantly about whether "Darwinists" are pushing for an atheistic worldview. There is no attempt to address the question of the religious and political background of the intelligent design movement's leaders and supporters.
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<h3>Bad Design Means No Design</h3>
By pointing out imperfections in living things it is somehow made apparent that there can’t be an intelligent agency behind it. This is really odd as it is basically a religious argument being made against Intelligent Design. The proponent of this argument is making a faith based assertion that God is perfect and hence incapable of bad design. ID makes no claim that the source of complexity is a perfect God incapable of imperfection. Write that down.

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<h3>Just what is evidence of design, anyway?</h3>
While true that ID ''tries'' to distance itself from religion, it is undeniable that the vast majority of ID proponents will put forward the Judeo-Christian [[God]] as the designer (ergo, it has ''failed'' to distance itself from religion). ID, as a concept, allows for anything to be the designer and to be involved in human evolution. Space [[extraterrestrial|aliens]], for example, are put forward as the ''most plausible case'' for ID; however, this is often mocked and outright dismissed in favor of religious concepts (as in the movie ''[[Expelled: No Intelligence Allowed]]''). So due to this, skeptics of ID can infer what the designer may be like by pointing out flaws in the "design". With such flaws, it is impossible for the designer to be perfect and with some flaws it is difficult for the designer to even be ''intelligent''.

This is not arguing from a religious aspect, it is merely asking the logical question: "who is this designer and why was it so incompetent in places?" It might be that this argument stings so much because it finds ID to be lacking ''on its own terms''.
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<h3>No Real Scientists Take Intelligent Design Seriously</h3>

Yes, they do. And even if they didn’t this is a logical fallacy called an appeal to authority. Ideas stand or fall on their own merits. Take a class in logic from a real logician at your nearest institute of higher learning and come back to us with a report card showing a passing grade. 

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<h3>No, no… REAL scientists</h3>
Too bad Dembski forgets that the people who will judge his idea on its own merits ''are'' real scientists. We must assume that "real" means "got their qualifications from a reputable institution, not a religiously-based diploma mill". Also it's not enough to be "a scientist" to be considered any kind of authority on the subject: a scientist's opinion on matters outside their field of expertise [[Ultracrepidarianism|is no weightier than anyone else's]] (would you necessarily believe what a biologist says about quantum mechanics?). The fact is that while some scientists will perhaps give ID the time of day, the vast, vast, vast majority of those in the field reject ID because, frankly, Natural Selection does a much better job of explaining the world.

:''See also: [[Project Steve]]
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<h3>“Evolution” Proves that Intelligent Design is Wrong</h3>

The meanings of evolution, from Darwinism, Design and Public Education:

#Change over time; history of nature; any sequence of events in nature
#Changes in the frequencies of alleles in the gene pool of a population
#Limited common descent: the idea that particular groups of organisms have descended from a common ancestor or multiple LUCAs.
#The mechanisms responsible for the change required to produce limited descent with modification, chiefly natural selection acting on random variations or mutations.
#Universal common descent: the idea that all organisms have descended from a single common ancestor (LUCA).
#Blind watchmaker thesis: the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, such as lateral gene transfer or endosymbiosis, are completely sufficient to account for the appearance of design in living organisms.

Creationists go with 1-4, with the change in 4 being built-in responses to environmental cues or organism direction as the primary mechanism, for allele frequency change, culled by various selection processes (as well as random effects/ events/ choice of not to mate/ unable to find a mate). The secondary mechanism would be random variations or mutations culled by similar processes. In other words life’s diversity evolved from the originally Created Kind, humans included. Science should therefore be the tool/process with which we determine what those kinds were.

Some but not ALL ID proponents go with 1-5, with the Creation change to 4 plus the following caveat in 5: Life’s diversity was brought about via the intent of a design. The initial conditions, parameters, resources and goal was pre-programmed as part of an evolutionary algorithm designed to bring forth complex metazoans, as well as leave behind the more “simple” viruses, prokaryotes and single-celled eukaryotes. This could be called “intelligent evolution.”

How are you defining evolution: blind watchmaker hypothesis? In that case there is not any positive evidence for that type of evolution based upon actual observation. What failed prediction would you consider to be adequate for falsification?

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<h3>Evolution is science, and far more powerful than ID.</h3>
While Dembski seems to be going on a tirade here about "defining" evolution, he forgets that ID proponents have some of the dodgiest terms going in order to move their goalposts about and wiggle out of questioning.
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<h3>Real Scientists Do Not Use Terms Like Microevolution or Macroevolution</h3>
This is urban legend, for such terms have been used regularly in the scientific literature.

Campbell’s Biology (4th Ed.) states: “macroevolution: Evolutionary change on a grand scale, encompassing the origin of novel designs, evolutionary trends, adaptive radiation, and mass extinction.”

Futuyma’s Evolutionary Biology, a text I used for an upper-division evolutionary biology course, states, “In Chapters 2h3 through 25, we will analyze the principles of MACROEVOLUTION, that is, the origin and diversification of higher taxa.” (pg. 447, emphasis in original).

These textbooks respectively define “microevolution” as “a change in the gene pool of a population over a succession of generations” and “slight, short-term evolutionary changes within species.”

...

The scientific journal literature also uses the terms “macroevolution” or “microevolution.” In 1980, Roger Lewin reported in Science on a major meeting at the University of Chicago that sought to reconcile biologists’ understandings of evolution with the findings of paleontology. Lewin reported, “The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the positions of some of the people at the meeting, the answer can be given as a clear, No.” (Roger Lewin, “Evolutionary Theory Under Fire,” Science, Vol. 210:883-887, Nov. 1980.)

...

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<h3>Who cares?</h3>
:''See [[macroevolution]]

The terms are used in biology, but it means something completely different to creationists. For creationists "macro" evolution CANNOT happen, while in ''real'' science it's just evolution at a different scale with no real boundary between the two. Macroevolution in biology refers to the ''evolution'' of organisms at a higher taxonomic level. Macroevolution in ID is just a magical buzzword that they can use to deny the importance of transitional fossils.

While real science and ID may share the same terms (specifically, ID has 
hijacked
 borrowed them from biology), their definitions of them couldn't be further apart.
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<h3>Intelligent Design Tries To Claim That Everything is Designed Where We Obviously See Necessity and Chance</h3>

Behe had this to say:

{{quotebox|Intelligent design is a good explanation for a number of biochemical systems, but I should insert a word of caution. Intelligent design theory has to be seen in context: it does not try to explain everything. We live in a complex world where lots of different things can happen. When deciding how various rocks came to be shaped the way they are a geologist might consider a whole range of factors: rain, wind, the movement of glaciers, the activity of moss and lichens, volcanic action, nuclear explosions, asteroid impact, or the hand of a sculptor. The shape of one rock might have been determined primarily by one mechanism, the shape of another rock by another mechanism.

Similarly, evolutionary biologists have recognized that a number of factors might have affected the development of life: common descent, natural selection, migration, population size, founder effects (effects that may be due to the limited number of organisms that begin a new species), genetic drift (spread of “neutral,” nonselective mutations), gene flow (the incorporation of genes into a population from a separate population), linkage (occurrence of two genes on the same chromosome), and much more. The fact that some biochemical systems were designed by an intelligent agent does not mean that any of the other factors are not operative, common, or important.}}

and

{{quotebox|I think a lot of folks get confused because they think that all events have to be assigned en masse to either the category of chance or to that of design. I disagree. We live in a universe containing both real chance and real design. Chance events do happen (and can be useful historical markers of common descent), but they don’t explain the background elegance and functional complexity of nature. That required design.}}

...

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<h3>Natural selection is not chance.</h3>
Dembski is here calling on Michael "Irreducible Complexity" Behe to prove a point. The point here is that Dembski and Behe claim that there is a fundamental part of nature that ''must'' be designed. They accept ''some'' naturalistic explanations (namely those that simply can't be denied) and put everything else down to magic. Behe's entire argument rests on one exceptionally flawed premise: "[[argument from incredulity|If ''I'' can't figure out how it evolved naturally, then it ''didn't'' evolve naturally]]".

Years ago, a lot of people would have said that the eye would be totally unable to evolve naturally. Now we have computer simulations, fossil evidence, better data and better trained biologists studying the problem and now scientists have a good and effective naturalistic explanation. The moral of the story is ''be careful what you label as magic, because some of us '''are''' watching closely''.
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<h3>What About the spreading of antibiotic resistance?</h3>

Micro-evolution. No “special ID explanation” required. Why, do you hold the misconception that ID proponents consider everything in evolutionary biology to be false?

Also, the existence of “superbugs” proves yet another ID prediction. Mutations are generally considered “beneficial” if they provide benefit to an organism in a particular environment. Meaning that the majority of these “beneficial” mutations are only beneficial in a limited sense. As in, they’re destructive (deleterious) modifications that are beneficial only in a limited environment. But they provide survival benefits in a limited environment, like blowing up a bridge in a war is beneficial in a limited sense. Darwinism requires not only beneficial mutations but constructive beneficial mutations in order to be feasible. We’re looking for constructive beneficial mutations that are not merely a reshuffling of existing genes via sexual recombination. Most of these superbugs are fortunately of the limited benefit type and will quickly be eradicated when exposed to normal conditions outside hospitals.

...

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<h3>No one is really making this argument!</h3>
Again, ID proponents resort to their shoddy definition of "macro" vs "micro" evolution. They do not [[moving the goalposts|explain the difference]]. They do not try to state ''why'' one can happen and the other cannot. They only use it to escape the inevitable conclusion that they are the same process on different scales.

When scientists prove a mechanism for the eye to naturally evolve, will this magically be reclassified as "micro" evolution? When a lab starts with a fly and evolves it into an ''entirely'' different species, will that be simply dismissed as "only microevolution"? ID only flourishes when it plays by its own rules, and these are ''not'' the rules of real science.
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<h3>What Do You Mean by “Constructive” Beneficial Mutations Exactly?</h3>
We are looking for examples of mutations that are not only beneficial in relation to fitness but also in relation to the progressive/positive creation/significant (> UPB) modification of existing CSI. But that’s a different thing than the “beneficial mutations” generally used in scientific literature. If there is a generally-accepted term that encapsulates what you are looking for I’m not aware of it. It’s not CSI in general since that could be negative in relation to fitness. For example, if I were to tack a spoiler (like on a vehicle) and a retractable anchor onto a bird I think that would not be too beneficial…

In Behe’s new book, the majority of the examples he discussed involved destructive albeit positively selected mutations, but not all. Behe also discussed the antifreeze glycoprotein gene in Antarctic notothenioid fish. In short, he says that it looks reasonably convincing as an example of Darwinian evolution, but that it’s a relatively minor development, and probably marks the limit of what Darwinian processes can reasonably be expected to do in vertebrate populations. So what we’re primarily looking for is the limitations on “constructive” positively selected beneficial mutations.

The Edge of Evolution is an estimate and it was derived from the limited positive evidence for Darwinian processes that we do possess. This estimate would of course be adjusted when new evidence comes into play or abandoned altogether if there is positive evidence that Darwinian processes are capable of large scale constructive positive evolution (or at least put in another category if it’s ID-based[foresighted mechanisms]). The bulk of the best examples of Darwinian evolution are destructive modifications like passive leaky pores (a foreign protein degrading the integrity of HIV’s membrane) and a leaky digestive system (P. falciparum self destructs when it’s system cannot properly dispose of toxins it is ingesting, so a leak apparently helps) that have a net positive effect under limited/temporary conditions (Behe terms this trench warfare). I personally believe that given a system intelligently constructed in a modular fashion (the system is designed for self-modification via the influence of external triggers) that Darwinian processes may be capable of more than this, but we do not have positive evidence for this concept yet. But that’s foresighted non-Darwinian evolution in any case, and even if there are foresighted mechanisms for macroevolution they might be limited in scope.

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<h3>What?</h3>
As usual, Dembski goes ahead and [[Straw man|defines evolution in ''his'' terms, then argues against it]]. If you will notice, he throws in CSI again, as if the concept was one the biologists use on a regular basis. This whole section basically rehashes the arguments that mutations can't be beneficial, and that evolution has a limit to what it can change. Both have long since been addressed.
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<h3>Intelligent Design proponents deny, without having a reason, that randomness can produce an effect, and then go make something up to fill the void.</h3>
ID proponents do not outright deny that “randomness can produce an effect”. Random variation is “guided” by environmental variables, which are pseudo-random in a sense. Meaning that once you have the environmental variables in place the funneling effects are predictable (deterministic to a point), but in nature what variables occur can be semi-random. ID proponents look to the relevant limitations of Genetic Algorithms and other computer simulations where Active Information via intelligent input is required. They also analyze the data for real world examples of Darwinian evolution and justifiably note that these processes are very limited in capability. In order to defeat our claim, a thorough stepwise indirect genetic pathway must be extrapolated from the data. This biological object must not only contain an Irreducibly Complex core set of components, but the informational content must be higher than 500 informational bits.

In the past Darwinists have attempted to discuss this topic but generally their imaginations fail to produce when their ideas conflict with basic engineering concepts:

Chance, Law, Agency, or Other?

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<h3>Making stuff up, are we?</h3>
Where are all of these calculations? Why haven't they been published in reputable biology journals? Oh, that's right, because they're meaningless.
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<h3>Intelligent Design is Not a Valid Theory Since it Does Not Make Predictions</h3>
Predictions of non-functionality of “junk DNA” were made by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980, Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions.

By contrast, predictions of functionality of “junk DNA” were made based on teleological bases by Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004).

These Intelligent Design predictions of are being confirmed. e.g., ENCODE’s June 2007 results show substantial functionality across the genome in such “junk” DNA regions, including pseudogenes.

These predictions are further detailed in Junk DNA at Research Intelligent Design.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
The ENCODE Project Consortium, Nature 447, 799:816 (14 June 2007) doi:10.1038/nature05874

There are other predictions, but the majority of them are within the scope of ID-compatible hypotheses.

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<h3>Not, uh.</h3>
Interestingly, the ENCODE projects paper mentions evolution multiple times and intelligent design not once.<ref>"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". ''Nature''. June 13, 2007. http://www.genome.gov/Pages/Research/ENCODE/nature05874.pdf.</ref> Just because the evolutionists were incorrect about a prediction does not make the intelligent design proponents right.

Besides, the relevant question here isn't whether ID has made a prediction or two that turned out to be correct (since [[stopped clock|any idea can make a true prediction purely by chance]].  The question is whether it consistently makes useful predictions: in other words, can we use it to do things that we couldn't have accomplished without the idea?
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<h3>The Evidence for Common Descent is Incompatible with Intelligent Design</h3>

Darwinists will sometimes phrase this objection as such: “please explain where common descent ceases to occur and design takes over.” Design IS the cause of common descent, which is not really a process, rather it is a pattern imputed to the observations of nature made by observers from the outside. Common descent has functioned more as an abstract heuristic akin to the practice of making sense of groups (who is in, who is out) and of then relating those groups by a process of elimination. Although it should be noted that ID is compatible with Universal Common Descent, Common Descent through multiple LUCAs, and other scenarios.

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<h3>Incompatibility</h3>
Citation needed!  It's not enough to [[Argument_by_assertion|simply claim]] that design is the cause of common descent without backing up that statement.  ID hasn't provided any evidence that design is the cause of changes in species, or of common descent, beyond "it looks designed".
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<h3>It is certainly true that evolution predicts only minor changes from generation to generation - but when you look at the cumulative effect of hundreds of millions or billions of replications then those many, many changes can incrementally lead to large changes.</h3>

You cannot simply stack small changes and–boom–you got something complex. That is not how it works in reality. A series of small changes have to come about independently, each having positive selective pressure, and then indirectly come together to form a new whole. This is called an Indirect Darwinian pathway. The reason a Direct Darwinian pathway is not an option is due to Irreducible Complexity since a Direct Pathway requires that a component have positive selective pressure for its function every increment. Darwinists do not like to tacitly admit that IC is a factor but that is why all current research is now directed upon Indirect Darwinian pathways. Unfortunately for Darwinists, that type of scenario is essentially relying on serendipity.

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<h3>It is certainly not true that the presence of a designer is required for any change from generation to generation, whether it is over one or millions or billions of replications.</h3>
You cannot say there's a designer and–boom–you got something complex. That is not how it works in reality and has certainly never been observed. A designer would have to have some sort of mechanism to "design" an irreducibly complex biochemical mechanism. While ID lacks that mechanism, evolution gives a pathway (whether you want to use the words "direct" or "indirect," which aren't really meaningful here). Looking at the genetics and protein sequences of a series of organisms you can determine the relationship between seemingly irreducibly complex biochemical machines. IDers do not like to tacitly admit that IC is just a definition and requires no explicit link between designer and the designed. Unfortunately for IDers, that type of scenario is relying on assumptions and begging-the-question-type arguments. Fortunately for biologists, evolution provides a means to generate new biochemistry.
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<h3>Macro-evolution *is* nothing but lots and lots of microevolution!</h3>
Actually, no, it’s not. That was the mainstream view years ago when the single-gene-single-function paradigm reigned. If that concept was true and did represent biological reality accurately then, yes, we would say that Darwinism is feasible. Discoveries during the last couple decades have made this concept very unlikely.

Quite frankly, the beliefs of many Darwinists are based upon an outdated simplistic viewpoint that is now known to be false. We believe this version of Darwinism is still taught and perpetuated because it is easier for people to swallow. In fact, the majority of ID proponents on this site used to believe it, including William Dembski and all the admins. And then we found out what modern science was telling us.

One of your fellow Darwinists was nice enough to admit this is not the case here on UD:

{{quotebox|One of the central tenets of the modern synthesis of evolutionary biology as celebrated in 1959 was the idea that macroevolution and microevolution were essentially the same process. That is, macroevolution was simply microevolution extrapolated over deep evolutionary time, using the same mechanisms and with essentially the same effects. A half century of research into macroevolution has shown that this is probably not the case. -MacNeill}}

But as to avoid being accused of unfairly quoting MacNeill out of context we must add that he personally believes that an “evolving holistic synthesis”, as he calls it, will emerge as a consensus in the coming years that will resolve the problems facing Darwinism. So now the real question is whether ID holds true in regards to this “evolving holistic synthesis” that is yet to be finalized. I don’t think anyone could say for certain at this point; it’s too early. It’s a different question with a potentially different answer.

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<h3>Macro/Micro</h3>
Actually, yes it is.

This is where Creationists (I'm sorry, '''ID''' proponents) ''compulsively'' change what they mean. First, there was no changing in species at all; species were species and were all created separately. Then they admit that change can happen, but it's all microevolution (which is usually defined as evolution within species level): breeds of dog for instance, some of which have physical differences way beyond animals that ''are'' different species. Then, when speciation was observed, they move the goalposts again, saying no, that's not macroevolution. They then prefer to bring up terms such as 
[[Baraminology|baramin]]
 "kind"; horses and zebras are the same "kind", tigers and lions are the same "kind", all fruit flies are the same "kind", all bacteria are the same "kind". To describe the terminology of ID as being fluid would be a massive understatement.

The problem is not with evolution, but with people like Dembski's understanding of evolution, or even their understanding of their own "science" of ID.

Also note, over the course of the whole entry, the point is repeatedly stated, but not once does anyone explain why it is the case or give any evidence for it.
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<h3>Nothing is Wrong with the Modern Synthesis!</h3>

The ideas that came from the modern synthesis concerning microevolution are as valid and as settled as any scientific ideas, although there may remain some tweaking to be done. Still, I think it interesting many a Darwinist's initial reaction is to defend the modern synthesis despite also claiming it’s been superseded. Why defend what you know to be wrong? Although, to be fair, I also think it weird that ID proponents are often preoccupied with personally attacking Darwin himself and/or outdated ideas.

Personally I think discussing RM+NS is like beating a dead horse even though there’s still many Darwinists that support it as the primary method for producing macroevolution. I’d rather move onto discussing these supposed “engines of variation”.

On “random mutations” and Allen’s claim that ID is using a strawman for evolutionary biology: ID proponents are using the term in reference to everything. For example, in Behe’s new book he lists all the mechanisms on one page but in general he uses “random mutations” unless a distinction needs to be made. Given that definition, these “engines of variation” would all be encapsulated under “random mutation”. But I agree that a better term should be adopted, since “random mutation” is often conflated with the over-simplification of the modern synthesis. One could also make this distinction with “non-foresighted mechanisms”.

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<h3>Modern synthesis</h3>
Science evolves; it progresses. It looks at the errors and where its current theories fail. It then regenerates, replaces, alters or adds to its theories. The next step is the same as before, to look at where the errors are and adjust the theories to fit. All Intelligent Design is capable of doing to adjust its 
theory
 hypothesis is to after-the-fact redefine the term "microevolution" to include more and more of the research biologists perform. Perhaps, one day, this evolution of ID will lead it to being indistinguishable from evolutionary theories as accepted by science? 

However, why do people stand by "old" and "outdated" theories? Because they still have use. To the pop-science oriented, science has theory A, then replaces it with theory B, which is then replaced by theory C. It's as if everything is thrown out and the universe alters significantly. In reality, it is more like science has theory A, and then adds to get theory A', then someone adds to make it A* or A<nowiki>''</nowiki>. The changes are small in real scientific alteration. The original theories are still valid to a degree, such as Newtonian mechanics, which is still perfectly and 100% valid when relativistic effects are low (in fact we use it all the time; NASA uses it to send probes to distant planets, for instance). Similarly with evolution, Darwin's original ideas still hold. The specifics may have changed, the individual evolutionary paths may have been analysed better, but the underlying principle of Natural Selection is ''still valid''.

At least Dembski understands that ID proponents and creationists that stick with what exactly Darwin said over a hundred years ago are silly at best (science, as stated, moves on and evolves).
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<h3>The Information in Complex Specified Information (CSI) Cannot Be Qualified</h3>

There are several ways of providing a quantitative number to CSI. First off, CSI references something else or it specifies something else that is functional. The objective functionality, independent of any viewer, is the Specification.

Now DNA is like a written and spoken language only it has meaning by referring to something else. We do not understand what 95% of DNA does but we definitely understand a large subset of it. It sets up a process to produce proteins. So we have these 64 letters in the DNA language called codons which are combinations of the DNA nucleotides. Since they are in threes and there are 4 possible options, there is a total of 64 combinations.

These codons specify one amino acid in each protein. This is all basic nowadays. A typical protein is 300 amino acids long and this requires 1200 nucleotides. It is possible to count the information content in such a protein or nucleotide string and perhaps there are some adjustments that can be made to each protein because most of the amino acids have more than one codon specifying it. Also some amino acids at different parts of the protein are interchangeable. So let's just say that the actual information content is less than the 1200 nucleotides in the gene specifying the protein. The total number of possible combinations in a 1200 series of nucleotides is 4^1200. As I said the actual number will be less.

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<h3>CSI</h3>
Way to not answer any questions about CSI. You haven't defined the terms, nor given other people a way to apply the term. You've talked about proteins and given basic genetic information. Nothing about CSI. Fail.

The really ironic thing here is that for all he talks about Complex Specified Information, he never ''specifies'' what it is exactly.  Perhaps it should be called Complex '''Un'''specified Information instead.
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<h3>What types of life are Irreducibly Complex? Or which life is not Irreducibly Complex?</h3>

It’s not life as a whole. Mechanical components of all life are Irreducibly Complex (IC). Not all components are IC nor do they qualify as Complex Specified Information (CSI). The question is whether unguided Darwinian processes (RM+NT, lateral gene transfer, symbiogenesis, reliance on hox genes, whatever) can produce IC and/or CSI components via Indirect Pathways. Unguided Darwinian processes perhaps are capable of producing components that are composed of 3-6 parts. But for comparison the flagellum is composed of 41 parts and the most observed we’ve ever heard of is 2 or 3. Again, part of ID research is determining the limits of unguided Darwinian processes. Agreeing that there are beneficial mutations and limited instances of small changes is in no way a threat to ID or an admission of some sort we have been saying this for years to deaf ears.

An IC machine cannot, by definition, be the result of a direct Darwinian pathway. Direct means that the steps are selected for the improvement of the same function we find in the final machine. IC makes a direct Darwinian pathway impossible. So, only two possibilities are left: either sudden appearance of the complete machine (practically impossible for statistical considerations), or step by step selection for different functions, and with the target function COMPLETELY INACTIVE for natural selection. This is a point that Darwinists tend to bypass. Darwinists may believe in indirect Darwinian pathways, because it’s the only possible belief which is left for them, but it’s easy to see that it really means believing in impossibilities. There is no reason in the world, either logic or statistical, why a complex function should emerge from the sum of simpler, completely different functions. And even granted that, by incredible luck, that could happen once, how can one believe that it happened millions of times, for the millions (yes, I mean it!) of different IC machines we observe in living beings? The simple fact that Darwinists have to adopt arguments like co-option and indirect pathways to salvage their beliefs is a clear demonstration of how desperate they are.

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<h3>The inferiority of irreducible complexity</h3>
Perhaps the biggest problem with irreducible complexity is the disconnect between irreducible complexity and the design. How does a biochemical "machine" being irreducibly complex imply that a designer formed the mechanism?

Irreducible complexity is really just the "science" of no imagination. Just because biologists haven't determined the step-by-step pathway through which an irreducibly complex machine came to be, does not mean that a designer created it. Nor does it mean that the scientists ''never will'' find the naturalistic mechanism. In short, the concept is [[special pleading]] at best and probably nothing more than an excuse to divert science spending to more worthwhile causes, like [[Abstinence_programs|abstinence-only sex education]] and [[Teach_the_controversy|confusing students in biology]].
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<h3>In the Flagellum Behe Ignores that this Organization of Proteins has Verifiable Functions when Particular Proteins are Omitted, i.e. in its simplest form, an ion pump.</h3>

I note you refer to the ion pump. An IC machine cannot, by definition, be the result of a direct Darwinian pathway. Direct means that the steps are selected for the improvement of the same function we find in the final machine. The very fact that you even attempt to make this argument showcases that your comprehension of IC is in error!

...

Now an Indirect Darwinian pathway for the flagellum would not only require that the code for various components come together (be co-opted), but that the code regulating that code be modified, the location/orientation be precise, modifications be made to the original code for these components, and that new code be generated. The reason new code is needed is because not all the components in the total system may have homologs or functions separate from the whole. For the flagellum there are currently 17 unique proteins with no known homologs (by the way, the T3SS and the subsystem in the flagellum are similar but not exactly the same; Behe is researching protein binding sites to see if there are limitations that may make indirect pathways not just unlikely but impossible). Then of course there are the external systems for controlling the usage of the flagellum…kinda useless to have an outboard motor but no way of using it. Never mind overcoming the pleiotropic nature of this code, since making these changes can and will often have adverse effects. As in, in order to have positive selection the changes being made not only have to pull together a functional flagellum but they can’t have a negative effect that is worse than the positive of having the functional flagellum. Invoking exaptation like a magic wand won’t help you here.

Now Behe certainly wouldn’t deny exaptation in general since he accepts universal common descent and this deals with a system being modified to deal with different environments. An example would be bird feathers, which are said to have evolved for temperature regulation and then later evolved for flight. But that still doesn’t provide a mechanism for this evolution.

Finally, we have been discussing the supersystem of the flagellum this whole time but we have neglected to focus on the subsystems. In its own right, the T3SS is fairly complicated, being comprised of [sic] 11 proteins. The problem Darwinists face is that Darwinian mechanisms have never been shown capable of even producing a system like the T3SS, never mind the full flagellum.

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<h3>The flagellum obsession</h3>
The flagellum argument has long since been addressed. The entire section by Dembski basically boils down to "[[argument from incredulity|I can't understand it, therefore it can't happen]]." If everything Dembski didn't understand didn't happen, the world itself might fall apart.  I myself don't really understand how computers work: how electricity running over wires and transistors and integrated circuits can be made to interact with humans, perform calculations, display graphics, etc.  Yet it would be senseless for me to conclude that computers ''don't'' work that way and there must be some intelligent mind controlling each computer.
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<h3>Darwinian evolution is a Vastly More Simplistic Argument than Intelligent Design</h3>

No, it isn’t. The hypothesis of a designer for obviously designed things is extremely simple, natural, and based on factual observation (the constant causal link between intelligent designers and their products in reality). I am really surprised by the inconsistent use of the concept of simplicity in discussions like [[Occam’s razor]] and similar. Everyone seems to have his own unjustified ideas of what is simple and what is not. Darwinian theory of evolution is not simple. It is a very complex and artificial attempt to justify something which appears designed, and has appeared designed for centuries to most rational beings, without admitting the existence of a designer. In fact, it’s expanded way beyond Darwin’s original mechanism of natural selection to incorporate a whole slew of potential mechanisms. That’s not simple at all…it keeps getting more and more complicated.

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<h3>Occam's razor</h3>
[[Occam's razor]] really only applies when ''all other things are equal''; even then, it's hardly an official law of the universe and is more like a judgement call. In the case of ID versus modern evolutionary theories, all other things are ''not'' equal, so Occam's razor wouldn't apply anyway.

Dembski is also getting confused about simplicity. The underlying principle of natural selection is painfully simple. From simple rules, very complex situations can appear, such as in The Game of Life or Langton's Ant. And thus, while Dembski and his colleagues may think that the world is complex, its workings are fundamentally simple.
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<h3>The Designer Must be Complex and Thus Could Never Have Existed</h3>

This is obviously a philosophical argument, not a scientific argument, and the main thrust is at theists. So I will let a theist answer this question: “[M]any materialists seem to think (Dawkins included) that a hypothetical divine designer should by definition be complex. That’s not true, or at least it’s not true for most concepts of God which have been entertained for centuries by most thinkers and philosophers. God, in the measure that He is thought as an explanation of complexity, is usually conceived as simple. That concept is inherent in the important notion of transcendence. A transcendent cause is a simple fundamental reality which can explain the phenomenal complexity we observe in reality. So, Darwinists are perfectly free not to believe God exists, but I cannot understand why they have to argue that, if God exists, He must be complex. If God exists, He is simple, He is transcendent, He is not the sum of parts, He is rather the creator of parts, of complexity, of external reality. So, if God exists, and He is the designer of reality, there is a very simple explanation for the designed complexity we observe.”

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<h3>Complex designer</h3>
Considering ID is not supposed to be creationism, it is interesting that Dembski addresses this question. Essentially, the answer is that God is simple because he just is. Way to handwave away the question; also, does it glorify God to call him "simple"?
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<h3>Intelligent Design is Completely Out of Date! It’s arguing against old idea and not modern evolutionary theory.</h3>

Not all Darwinists believe that the principal mechanism for unguided evolution is the same thing. When an ID proponent refers to “Darwinism” we are referring to all proponents in all “camps” who are supporting unguided evolution. If we refer to you as a “Darwinist” it is because the term encompasses all advances in modern evolutionary theory and/or we’re not sure what camp you consider yourself a part of. We are not referring to the original hypothesis as advocated by Darwin himself, which has been termed selectionism. Advocates of the “modern synthesis” formed in the 1930s are commonly referred to as Neo-Darwinism, which to this day is the largest camp by far. ID proponents will often shorten the name of this mechanism down to “RM+NS”. But as the USA-based National Research Council recently published, “[n]atural selection based solely on mutation is probably not an adequate mechanism for evolving complexity.” Instead, the newer camps believe that lateral gene transfer, endosymbiosis, and other potential mechanisms are possibly the mechanisms for creating complex genomes.

The Neo-Darwinist camp is still probably the biggest of all the Darwinist camps but people are likely to start abandoning “Neo-Darwinism as the primary mechanism” in droves. The Neo-Darwinist camp being so large is probably primarily due it being the only major version of Darwinism mentioned in higher education unless your degree program is focusing on evolution. And of course the media almost never differentiates between the various camps. So once education and media catch up we see the Neo-Darwinist camp shrinking even more rapidly.

Also, we differentiate by camp based upon where the individual Darwinist puts their “Darwinian mechanism/process” emphasis. This means that ID proponents are not claiming that all these Darwinian mechanisms cannot “help” each other: where one is weak/limited the other may not be. Unfortunately, this can be confusing since a good (short) name that encapsulates all these other camp’s ideas has not been formulated. Some Darwinists just call it “modern evolutionary theory” but that is too long for common usage and it does not make known the distinctions.

...

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<h3>Just how out-of-date is it?</h3>
Um...ok.  This going somewhere?
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<h3>Intelligent Design Does Not Do Research</h3>

Scientific research takes money and institutional support. Most people do not have the money to go out and build a multi-million dollar lab they can run themselves. The Discovery Institute has been funding a little research, and the CRS and ICR have been funding Creationist research, but other than that there is not much money. Discovery Institute’s Center for Science and Culture (its program on intelligent design and evolution) only spent $1.2 million in 2003. In 2004 it spent the same, and in 2005 it spent $1.6 million. Indeed, the budget for the entire Discovery Institute, including expenditures on non-intelligent design programs on transportation, technology, and other topics, has never reached $5 million. In 2003, the Institute as a whole spent $2.5 million. In 2004, it spent $3.5 million, and in 2005 it spent $3.9 million. These facts are publicly available for anyone to check on the Institutes Form 990s posted at www.guidestar.com.

The latest research by ID proponents is attempting to ascertain the exact limits of unguided Darwinian processes and convenient scenarios. It should be noted that Creationists can conduct research that advances Intelligent Design without directly supporting the preferred hypotheses of ID proponents which may contradict Creationism. In return, Intelligent Design proponents, who may not advocate Creationism, can produce research that may be supportive of Creationism. While there can and will be overlap the issues should not be conflated.

[Dembski gives a list of ID researchers here]

You must also take into account persecution of ID proponents. For example, Dembski and Marks were forced by Baylor to return a research grant due to the implications of the research possibly being in favor of ID. ID proponents desire to increase the amount of research being done but Darwinists usually block the way. If you are making this argument then how can you not see the hypocrisy in saying that ID proponents should do research then blocking every attempt to do so?

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<h3>"Researching" doesn't make it right.</h3>
It is important to note that the scientific community, while a difficult community to enter, will typically have someone who is willing to fund promising projects that may produce interesting results. That no one funds ID's "research" is more telling than their lack of results and publications.
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<h3>Intelligent Design Cannot Be Falsified</h3>

Now Dembski has written a paper which shows that evolutionary search can never escape the CSI problem (even if, say, the flagellum was built by a selection-variation mechanism, CSI still had to be fed in).

If I may interpret what I think he’s saying: that even if an Indirect Stepwise Pathway was found to be capable ID would not be falsified completely, as the problem would then be shifted to the active information injected at OOL. Essentially, this would be a combination of Design and a Chance Hypothesis.

At this point if Necessity would need to be shown to be capable creating CSI in order to falsify ID. Since this instance of Necessity is not known what is being looked for is an “unknown law”.

Let’s say we found a 2001-style monolith on the moon and all the planets. Design would likely be inferred. But suppose later on we discover unknown processes (a Law) that is observed to create these monoliths in space as an emergent property of an interplay of processes. ID theory would be revised to take this Law into account.

Similarly, formalized design detection in regards to biology is open to falsification based upon new observations. It’s possible there is an unknown Law operating upon biology. If evidence of this unknown Law were found, ID theory would need to be revised. The limits of this Law would be analyzed. For example, this Law may only operate under limited circumstances and be capable of producing limited forms of complex specified information. Now this is only in regards to self-replicating life; obviously a separate unknown Law or event would need to be found for OOL. But if positive evidence is uncovered that these Laws are capable of operating uniformly then the entire ID scientific program in regards to biology is kaput.

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<h3>Show me Mr. Designer Doesn't Exist!</h3>
The monolith example is a [[red herring]] used to hide ID's faults. 

There has never been any mechanism proposed through which the designer designs, and the identity of the designer is always just stated to be "not God" (except when ID proponents are speaking to a religious audience, in which case it's stated or implied to be "our God". How do you propose to show that a designer doesn't exist? And how do you show that a designer didn't design a life form if you don't say how it formed a life form?
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<h3>ID Proponents Wrongly Claim that Natural Selection Does Not Work</h3>
Allen MacNeill (and other biologists) actually tries to break natural selection into several different “neat” categories to fit the evidence that is consistently found in the fossil record (very sudden appearance, then rapid diversity, then slow decline in diversity over periods of time.) Let me explain.

All naturally occurring populations exhibit what Fisher called continuous variation. That is, a range of variation in various traits that, when plotted in Cartesian coordinates, approximates a normal distribution (bell-shaped curve). In a trait that exhibits continuous variation, most of the individuals exhibit the trait at a value reasonably close to the mean, with a relatively small number of individuals exhibiting relatively large or relatively small values for that trait.

An example is height in humans, which is often illustrated in introductory biology texts with a group of students arranged along a football sideline in order of height. There are a few very short and a few very tall people, but the vast majority form a bulge in the middle of the curve. As noted by Eric that major problem is with the “engines of variation”.

Given a population that exhibits continuous variation for a trait, it is claimed that there are three different patterns of natural selection that can result:

Stabilizing selection, in which individuals from both extreme “tails” of the normal distribution are not preserved over time (i.e. they do not have as many offspring that survive to reproduction), compared with those in the middle bulge of the curve. Under such conditions, the mean value for the trait does not change over time (hence the term “stabilizing selection”). In our example of height, stabilizing selection would be the result if individuals of average height had the most surviving and reproducing offspring (assuming that height is [[heritable]] from parents to offspring, of course).

Directional selection, in which individuals from one (but not the other) extreme “tail” of the normal distribution are not preserved over time (i.e. they do not have as many offspring that survive to reproduction), compared with those in the middle bulge of the curve. Under such conditions, the mean value for the trait changes over time, shifting toward the tail of the curve that includes the surviving individuals (hence the term “directional selection”). An example would be a population on an island all becoming pygmies over time.

Diversifying selection, in which individuals from the middle of the range (but not either extreme “tail”) of the normal distribution are not preserved over time (i.e. they do not have as many offspring that survive to reproduction), compared with those at the extreme tails of the curve. Under such conditions, the mean value splits and becomes bimodal, with two new mean values increasing in frequency, and the old mean value disappearing. This process would eventually (depending on the intensity of selection) produce two phenotypically different populations where one had previously existed (hence the term “diversifying selection”).

Thus, with these different versions of natural selection Darwinism becomes unfalsifiable. For they can explain both rapid diversification of a fossil type and then can explain lack of diversity of fossil type thereafter. He can explain anything he wants in the fossil record whenever he wants his theory to fit the evidence. i.e. his “new” theory has greater weight than the evidence has to falsify it.

I agree that some ID proponents may go too far, and many forget that Natural Selection is the non-random component of Darwinism. I know some ID proponents have argued in the past for an intelligent mechanism for the finch beaks, but we can look at GAs and see that fitness functions do work when properly balanced (which is active information).

The problem is that Darwinists presume this balancing act and thus that natural selection is capable of operating uniformly. As in, for ALL targets in a search space there exists environmental factors capable of creating diversifying or directional selection to the extent that features become fixated within a population. I have no problem with the assertion that this works for SOME cases, just not ALL.

The reason I think this is an issue is since selection usually relies on environmental factors (I say usually since there is artificial selection like with dogs). While some factors are generalized, some factors must be very specific in order for the funneling effect to work. What if, like with these peacock feathers, the factors are very rare or don’t even exist? That means that in order for Darwinism to work not only does Functional Complexity have to emerge it must be paired with a rare event that offers selective pressure.

Now ID proponents don’t dispute the notion of stabilizing selection. They dispute the notion that there’s a kind of selection other than stabilizing selection that can operate successfully to the point of macro-evolution. This does not mean that selection in general does not happen per se (think finch beaks, blind cavefish, malaria, ice fish, etc.) but Berlinski would probably say it’s not special enough that should not warrant a separate categorization. Or at least that directional selection is exceedingly rare and can only operate under limited conditions/environments and thus for a very short amount of time (or at least it better be short lived…directional selection tends to decimate a population as was seen with the finches). Personally I’m fine with people making these categorical distinctions since they’ve only been shown to be capable of trivial changes.

Now as I’ve pointed out before the major issue is that natural selection is essentially a funnel, and it must be balanced in order to produce results. For an example, a while back I had an experiment with a GA that performed word searches. Going from memory here, so short version is that there were multiple versions of the fitness function: a) pseudo-random search b) a function that attempted to emulate Darwinism c) a function that incorporated some active information about the target d) explicit directed front-loading. The target was less than 200 informational bits but only C and D were capable of finding it. The most difficult target at 360 informational bits required D.

The point is that selection must be constrained and balanced long enough that the trait becomes fixated. The problem with the finch example is that once the environment changes back to normal the finch population also reverts back to being a mixed population based upon continuous variation. As in, the changes purportedly funneled by directional selection don’t stick (they are not fixated). Some Darwinists like to say that in order for such changes to fixate that the environment must be permanently altered as well. Well…in the finches case it’s apparent by their dwindling numbers that this might likely cause extinction of that population within that environment. Even if they did survive and the trait did fixate within the population it’s unknown whether the finches would permanently lose the ability to produce beaks of different sizes if the environment changed once again far off into the future.

...

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<h3>Just how well does natural selection work.</h3>
Translated, this passage boils down to: ID accepts evolution as laid out in modern biology, except in those spots where it seems hard to believe evolution could be the cause, and in those circumstances ''magic'' is the best explanation.
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<h3>Intelligent Design Makes No Scientific Observations</h3>

While Darwinists have been happy to rely on story-telling Behe went and tried to find evidence for what Darwinian mechanisms are known to be capable of. The result of that research was published recently in [[The Edge of Evolution]].

Behe’s latest work of analyzing what billions of trillions of replications of p.falciparum accomplished in the way of generating novel complexity without benefit of intelligent agency supports the prediction that only intelligent agency is capable of producing complex specified information. Random mutation and natural selection is almost universally regarded as a process which can generate complex machinery de novo. In principle this might be true - given enough time and opportunity to overcome statistical improbabilities and presuming that genetic entropy (deleterious mutations) do not outpace positively selected Darwinian processes. In practice all observations says there has not been sufficient time and opportunity. The universe is not believed to be either infinite in temporal or spatial dimension and the earth environment is far more limited. The modern synthesis, RM+NS, is the front runner for an alternative mechanism to intelligent agency. Under close observation in a fast eukaryote reproducer, in orders of magnitude more reproduction than all the mammals that ever lived, RM+NS failed to even remotely approach generating any of the genomic complexity that distinguishes modern mammals from their reputed reptilian ancestors. This is a more compelling example of a successful prediction for ID than was the confirmed prediction of cosmic background radiation was for the big bang theory. Possibly further research will reveal a reason why RM+NS failed to produce any significant complexity in p.falciparum but as it stands now there is no good explanation for the absence of any significant new complexity with such vast opportunity for it to self-organize.

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<h3>The BS of Behe</h3>
Behe's work comes down to an [[Creationist_mathematics#BIG_NUMBERS|argument by big numbers]], which is more ''fallacy'' than ''evidence'' for his position.  Also, as a side note, it would be more accurate (though still a bit of an overstatement) to say that intelligent agency is an alternative to the modern synthesis, not the other way around.
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<h3>Behe is Jumping to Conclusions. p.falciparum Did Not Evolve Because It Did Not Need to Evolve. In Other Words It is So Perfect Already That It Cannot Improve Upon Itself.</h3>

This answer, aside from being in opposition to neo-Darwinian postulates of random evolutionary trajectories (the answerer seemed to be channeling Lamarck) is quite wrong in the face of the facts of what p.falciparum “needed” in the way of differential reproduction.

Examples:

1. p.falciparum is excluded from a vast reproductive opportunity because it cannot survive in sub-tropical climates. Extending its range into temperate climates would vastly increase its reproductive potential. Evidently the necessary mutations for this require more than just a few interdependent mutations. It failed to increase its range in billions of trillions of replications.

2. The human-produced and administered drug chloroquine has killed billions of trillions of individual p.falciparum yet in billions of trillions of mutational opportunities to resist this drug, which requires just a few point mutations, it only found a way to resist, through random mutation and natural selection, about 10 times. In none of those 10 times did the RM+NS improved version of the parasite pass the improvements on into the parasite population at large.

3. A hemoglobin mutation in humans (sickle cell) confers resistance to p.falciparum (causing it to starve as the mutated hemoglobin clogs up its digestive mechanisms). Again in trillions of mutational opportunities p.falciparum failed to evolve any means of surviving in the sickle cell environment. Evidently this too requires more than just a few chained interdependent mutations.

How does modern evolutionary theory, with all its glut of potential Darwinian mechanisms beyond the modern synthesis’s RM+NS, explain these failures to evolve complex structures under intense selection pressure when given far more opportunity to evolve than all the mammals that ever lived?

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<h3>Behe 2</h3>
The evolutionary trajectories posited are not random. They depend on the selective pressures exerted by environmental change. The changes aren't random either: the environment is a chaotic system of chaotic systems. Borderline impossible is not the same thing as random, which Dembski should know from studying mathematics. His claim otherwise makes this a straw man.

''Plasmodium falciparum'' hasn't expanded to other environments because it hasn't needed to. There has been nothing in its native environments that would force it to adapt to colder climates. Into the last century it infected vast numbers of people and humans could do very little to exert any selective pressure against it. It still does infect huge numbers of people.

Chloroquine exerted a powerful selective pressure against ''falciparum'' in its time. It is no longer nearly as effective as it once was because the protozoan, over tens of thousands of generations, evolved resistance to it (as even Dembski admits). His next claim, though, that this resistance never spread, is an out-and-out lie. Mosquitoes can pick up malaria from infected people and transmit it to new people, conferring a huge advantage on resistant ''falciparum'' populations that we'll let Wikipedia describe:

{{cquote|''Since the first documentation of P. falciparum chloroquine resistance in the 1950s, resistant strains have appeared throughout East and West Africa, Southeast Asia, and South America. The effectiveness of chloroquine against P. falciparum has declined as resistant strains of the parasite evolved. They effectively neutralize the drug via a mechanism that drains chloroquine away from the digestive vacuole. Chloroquine-resistant cells efflux chloroquine at 40 times the rate of chloroquine-sensitive cells...''<ref>{{wpa|Chloroquine#Resistance_in_malaria}}</ref>}}
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<h3>ID Proponents Talk a Lot About Front-Loading But Never Explain What It Means</h3>

In engineered systems various possible contingencies are anticipated and processes are put in place to deal with them if and when any particular contingency actually arises in the future.

These forward looking predetermined responses are “front loaded” - put in place before they are actually needed.

Chance & necessity is a reactive process that cannot plan ahead. Intelligent design is a proactive process that can plan ahead.

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<h3>Rearending frontloading</h3>
Basically, if something ''does'' spontaneously mutate a useful new feature (for example, [[Richard Lenski#Lenski's long-term E. Coli evolution experiment and intelligent design|the ability to metabolize citrate]]), ID will claim "Well, <strike>God</strike> The Designer put that ability there when He created them, ready to activate when the time was right! Really!"
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<h3>Lenski’s Research on Citrate-Eating E. Coli Refututes Behe’s Edge of Evolution Hypothesis</h3>

...

Darwinists should stop pretending they have the current strongest explanation. I’ll fully acknowledge they’re currently formulating a response in the form of continued research, new models, and such but the mere fact is that they’re missing all the major parts to their explanation. This might change in the future, but it may not.

Or at least the situation hasn’t changed based upon this recent conversation where I asked for the functional intermediates in the indirect stepwise pathway to be named…and was never answered. Comment #203 summarizes that discussion, and should be read at full length, but I thought this was the kicker:

{{quotebox|if the final function is reached through hundreds of intermediate functions, all of them selected and fixed, where are all those intermediates now? Why do we observe only the starting function (bacteria with T3SS) and the final function (bacteria with flagella)? Where are the intermediates? If gradualism and fixation are what happens, why can’t we observe any evidence of that? In other words, we need literally billions of billions of molecular intermediates, which do not exist. Remember that the premise is that each successive step has greater fitness than the previous. Where are those steps? Where are those successful intermediates? were they erased by the final winner, the bacterium with flagellum? But then, why can we still easily observe the ancestor without flagella (and , obviously, without any of the amazing intermediate and never observed functions)?}}

gpuccio was also gracious enough to assume the T3SS as a starting. Dave pointed out this long ago:

{{quotebox|The gist of it, as I recall, is that the t3ss appears on small number of bacteria that prey on eukaryotes. It’s a weapon used to inject toxins into the prey. In the meantime the flagellum appears on a large number of bacteria that don’t prey on eukaryotes. Thus saying that the t3ss predates the flagellum is like saying that anti-aircraft missiles predate aircraft. Non sequitur. Flagella were useful to bacteria before eukarotes appeared but a t3ss would be useless before then.}}

...

Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events,” he says. “That’s just what creationists say can’t happen.”

What a nice PR strategy. Assert their opponents making certain claims that they are not, then blow away that fake claim. AKA Strawman. Yet we’re never given the space to defend ourselves against such outrageous tactics.

...

The fact that the opponents of Behe’s book find the need to repeatedly lie and misrepresent the book (Carroll and Miller) or avoid the subject matter altogether (Dawkins) shows exactly how good Behe’s book is. In spite of having more reproductive events every year than mammals have had in their entire existence, malaria has not evolved the ability to reproduce below 68 degrees. Nick Matzke’s explanation for this was that “in cold regions all the mosquitoes (and all other flying insects) die when the temperature hits freezing.” Think about it. Malaria cannot reproduce below 68 degrees Fahrenheit. Water freezes at 32 degrees Fahrenheit.

Musgrave and Smith have asserted that their research into HIV has disproved Behe’s hypothesis. To illustrate how out to lunch Musgrave and Smith are on Behe’s Edge of Evolution, on page 143 Behe writes that the estimated number of organisms needed to create one new protein to protein binding sites is 10^20. Further down the page, Behe notes that the population size of HIV is, surprise, within that range. So according to Behe’s own thesis, HIV should be able to evolve a new protein-to-protein binding sites. So along come Smith and Musgrave, point out a mutation clearly within Behe’s thesis, and then declare victory when in fact they have not contradicted Behe at all. All Behe needs to do is update his book to include that example.

How about an actual example where a more complex organism is less fit than its simpler counterpart? Depends on the complexity being looked at it, does it not? Let’s take a look at TalkOrigin’s example of people with “monkey tails”. I have no problem calling that “complexity” in a generalized sense. As in, not CSI, but a continuation of a process beyond its normal termination. I’m not sure what positive effects they do have. From what I remember they’re not articulated and cannot serve as an additional limb. But I’m pretty sure they’d act as the opposite of a peacock’s feathers, (which, BTW, has its own issues), dramatically reducing those individual’s chances of reproducing. Ditto goes for additional/non-functioning mammary nipples and other examples that turn off the opposite sex.

The situation is complicated enough that there can’t be blanket statements. There can be increments in complexity where the tradeoff is more positive than negative. But that’s why ID doesn’t have blanket statement…there is a complexity threshold. And that’s why Behe is trying to find an “edge of evolution”. While an estimate has been arrived at I don’t think that “edge” has been found yet. Personally I think it “might” be greater than where some ID proponents envision it to be. Perhaps the “true edge” is around 6 steps in an indirect stepwise pathway. But I could be wrong.

The perspective of ARN:

There are several observation that should be made before reaching general conclusions. The first relates to the machinery needed to metabolise citrate. The system to do this is already largely in place, but one enzyme is lacking. This is the comment from Mike Behe: “Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it’s not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a “citrate permease” which can transport citrate from outside the cell through the cell’s membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.”

Consequently, it is at least worth asking the question whether the E.coli bacterium had, in the past, lost the ability to metabolise citrate and what we are now seeing is a restoration of that damaged system. If this were the case, we should not be talking about “a major evolutionary innovation” but rather about the way complex systems can be impaired by mutations.... it demonstrates a major problem for those evolutionists who want to claim Darwinism can achieve major transformations. These mutations are not only rare, they are also useless without the pre-existence of a biochemical system that can turn the products of mutation into something beneficial.

...

The main point remains: at this time Darwinism does not have a mechanism observed to function as advertised. Should we continue research on proposed engines of variation? Definitely. When Edge of Evolution was released I believe I said that would make a good follow up (considering each proposed mechanism one by one, and of course their cumulative effect).

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<h3>Lenski, Behe</h3>
...
Clearly the [[Lenski affair]] burns ID proponents, to the point that they'll go to some lengths to try to refute what happened.  This is, of course, because it showed [[Richard_Lenski#Lenski.27s_long-term_E._Coli_evolution_experiment_and_intelligent_design|things they said couldn't happen]].
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<h3>The Evidence for Gradualism in the Phylogenetic Tree of Life is Overwhelming</h3>

I suggest you read the latest studies:

Bushes in the Tree of Life

recent analyses of some key clades in life’s history have produced bushes and not resolved trees.

The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.

Wolf and colleagues omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom

The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology.

I think it would help the conversation to differentiate between Darwinian Common Descent and Common Descent compatible with ID hypotheses (which is fine with the above picture of bushes and not a consistent TOL). For example, you wouldn’t expect to find the same information being used in divergent lines from a Darwinian viewpoint if they’re geographically isolated or if the divergence supposedly took place a very large amount of time before.

ID proponents typically interpret homology as compatible with universal common descent, common descent from multiple LUCAs, or Designer Information Reuse (which is itself compatible with multiple scenarios). Instead of resolving a tree we’re getting bushes since we cannot find the gradual informational links that would be expected of Darwinian Common Descent. Continuing the theme of “islands of functional information”, these bushes could also be called “archipelagos of functional information” which must be bridged by informational leaps. Designed mechanisms could bridge (or traverse) these informational leap, thus producing Designed Common Descent.

Wolf and colleagues even discuss the “high frequency of independently evolved characters” aka convergent evolution. Another thing that ID proponents predicted is homologous information where none would be expected if Darwinian mechanisms were responsible for macro-evolution. Like the platypus, for example, whose genome is a patchwork of mammal, reptile, and bird.

Chromosomal sex determination in the platypus was also discovered to be a combination of mammal and bird systems. Yet TalkOrigins says:

birds are thought to have evolved from dinosaurs in the Jurassic about 150 million years ago, and that mammals are thought to have evolved from a reptile-like group of animals called the therapsids in the Triassic about 220 million years ago. No competent evolutionist has ever claimed that platypuses are a link between birds and mammals.”

Oops.

Often the the convergent evolution storytelling card is played…you’d think Darwinist would have run out of cards in that deck by now. Universal common descent from a single LUCA may be true itself but the historical narratives we have now may not be true themselves.

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<h3>Phylogeny 1</h3>
ZOMFG. A scientist was wrong about something once. [[Science was wrong before|How can we ever believe ANYTHING Science says, ever AGAIN!?!?!?]]
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<h3>Even if the Tree of Life is Not Gradual We Still See a Bottom-To-Top Pattern as Darwin Predicted Would be Found</h3>

The real question is: Does the fossil record confirm or contradict the bottom to top pattern?

Here is James Valentine’s answer:

{{quotebox|Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas.}}

Now Valentine is a believer in a Darwinist approach to evolution so I would assume that the above quote is not biased.

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<h3>Phylogeny 2</h3>
Funny, he also said the following:
{{quotebox|Darwin had a lot of trouble with the fossil record, which did not seem to support a pattern of gradual and incessant morphological change such as he envisioned. In chapters 10 and 11 of ''On the Origin of Species'', "On the Imperfection of the Geological Record" and "On the Geological Succession of Organic Beings," Darwin rationalized the lack of detailed support for his ideas, essentially by attributing it to the spottiness of the fossil record. Today the fossil record is far better known than in Darwin's time, and methods have been developed that help circumvent its imperfections.<ref>https://books.google.com/books?id=DMBkmHm5fe4C&pg=PR4&lpg=PR4&dq=On+the+Origin+of+Phyla:+Interviews+with+James+W.+Valentine&source=bl&ots=VRpX2fy7Ig&sig=pD3xDV9Mw3KGzBjdpiQ78OWmlj0&hl=en&sa=X&ved=0ahUKEwiLtuyOjt7QAhXhqlQKHZd9B80Q6AEIQTAG#v=snippet&q=darwin%20had%20a%20lot%20of%20trouble&f=false</ref>}}
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<h3>Lateral (Or Horizontal) Gene Transfer (LGT) is Strong Evidence Against ID</h3>

When you think about novelty, think about both morphological and genetic novelty. James Valentine, the most knowledgeable of all paleontologists on the Cambrian Explosion, makes the argument that the novelty of body forms in the Cambrian came about through relatively simple changes in patterns of gene expression. This would presumably be because of the modular nature of their body plans.

Valentine sounds like is describing a common ID-compatible hypothesis. Whence came the modularity? And foresighted mechanisms? Why should ID proponents reject the capabilities of LGT if the system is designed to take advantage of it? (Although I will add that so far evidence for the extent of the capabilities of LGT is fairly limited yet it is assumed to be very active regardless.)

I’d also like to add that there probably should be made a distinction between Undirected/Non-Foresighted LGT and Active/Foresighted LGT. Now it’s possible that a Designer could build a system in expectation of undirected processes, but at least one ID-compatible hypothesis would expect A-LGT. For example, viruses as a whole could have once contained the functionality of networking all organisms and triggering macro-evolutionary events.

The problem with such functionality is that it would be expected to be highly susceptible to deleterious mutations since it’s not necessary for survival and thus this particular biosphere system for evolving would degrade with time. Eventually we’d be left with simple replicators totally focused on self-survival as we see today. BUT since they’re such fast replicators we might hope that some remnant of this functionality might survive.

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<h3>LGT</h3>
Is this going somewhere?
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<h3>Symbiosis Theory as Promoted by Lynn Margulis is Evidence Against ID</h3>
We should probably not consider symbiosis to be a subset of Darwinian mechanisms. But if you insist that we define it as such I have no problem with conceding that under your definitions that a subset of Darwinian mechanisms is “apparently” capable of producing macro-evolution. But it’s not like you can define ID away…

The available examples seem to interestingly show that there is very active interaction between host and symbiont, and different forms of adaptation. Frankly, nothing of that seems to have the characteristics of random variation. I would not call those things “macroevolution”, or, if we want to call them that way, they are examples of a kind of “macroevolution” which is very different from the classical form.

Here we observe active adaptation between existing species, and the biologic information for the expressed functions is already there, it is rather actively mixed, shared, and in some way readjusted. The process, although more complex, seems similar to lateral gene transfer between bacteria. Shall I remember that LGT is a common procedure, and that it is in some way part of the natural functions of bacteria? Symbiosis too is a common event in nature. It is a form of cooperation, not of generation of new functions from random events.

It’s logical to consider exchange of information and symbiosis as important elements in the modeling of living beings. They are, from bacteria to humans. But that changes nothing in the fundamental problem of the genesis of information.

Biological information must exist before it can be exchanged or remixed. All biological information, at its fundamental level, cannot just be the product of “exchange”. Proteins with their functions, the DNA code, regulation networks, complex molecular machines, body plans, transcriptome regulations, and so on, all must exist and work, and then they can sometimes be exchanged and/or shared between different living beings. So, arguments such as symbiosis and similar mechanisms are of no help to explain the origin of information.

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<h3>Symbiosis</h3>
Or this?
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<h3>Final Warning</h3>

If you are making the above arguments your understanding of the subject matter is in error. The simplistic view of Darwinism of the past that you apparently adhere to is wrong. The arguments you are attempting to regurgitate will quickly earn you scorn. Please read the scientific literature produced by both Darwinists and ID proponents before continuing your association here at Uncommon Descent.

On a humorous note, in 2007 the UD database suffered corruption by which this page was hit by a series of point mutations to the text. All of them were deleterious. Of course, we have cleaned them up by erasing those remnants of Darwinian processes.

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<h3>We don't contribute to your blog anyway.</h3>
"Whatever you're going to say, you're wrong. So shut up and go away so we can do BIBLE SCIENCE."

The really humorous part of the incident he describes here is that the "mutations" happened to his blog, which we would all agree is intelligently designed (at least in the sense that it was designed by an intelligent being).  It's to be expected that any random changes made to an intelligently designed item would be deleterious, since such an item has usually been fine-tuned by its designer.  Something which has come about through natural selection, on the other hand, is much more likely to benefit from random changes—and so, this incident which he tries to use as a cheeky comeback to critics of Intelligent Design is in fact an argument ''against ID''.
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==See also==
*[[Uncommon Descent]]
*[[Conservation of Information in Search - Measuring the Cost of Success]]
*[[The Search for a Search - Measuring the Information Cost of Higher Level Search]]
*[[Efficient Per Query Information Extraction from a Hamming Oracle]]
*[[Barry Arrington]]

==References==
{{reflist|2}}
{{crebox}}

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[[Category:Refutations]]
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