The rational person should place in a hopper all explanations, that are not disproved, for a given phenomenon that is without definitive explanation.. That the explanation is 'scientific', judged to be 'rational' or does or does not meet any other preconceived notion of a 'reasoanble explanation' is not important. If it explains the phenomenon and is not disproved, it should be included. To do otherwise is actually irrational. It is akin to insisting that reality conforms to one's expectations of it.
From these, one should be selected, based upon a judgement of strength of evidence, as a working hypothesis. This situation ends when either one explanation comes to dominate the evidence or all but one explanation has been eliminated, the famous Sherlock Holmes method. At that point it becomes doctrine in the current world view and is generally referred to as a fact. Many 'scientists' would argue that this 'working hypothesis' approach is unscientific. Yet, they do it all the time. That the Universe came into being through mechanistic processes is an example of one of their working hypotheses. There is actually no significant evidence to support the assertion.
Evolution as a mechanism by which speciation takes place is a fact, as defined above. That it is the only mechanism that caused the simplest of self-replicating molecules to transform into the riot of morphological and biochemical variation we see today does not rise to that level. In fact, it may not even properly be chosen as the current working hypothesis over the full spectrum of events. That there was intelligent and volitional intervention in the process is a possible explanation that needs to be placed in the hopper.
The above is far from a comprehensive treatment of Intelligent Design. In fact, without precluding the possibility that there are more, there are at least three fundamental questions that relate to Intelligent Design. They are 1) How did the Universe come into existence with physical parameters that seem to be carefully designed to allow the emergence of complexity? 2) How did the first self-replicating molecules come into existence? and 3) How do adaptive traits that require mutations on multiple gene sites and that do not appear to have mechanisms for incremental evolutionary reward come into existence?
In each case Science cannot provide us with a definitive answer. In other words, the questions do not have answers that rise to the level of 'fact'. Rather, we find ourselves with a basket full of speculations that are not disproven. One of these speculations is that it results from intelligent and volitional intervention. The least problematical explanation should be the working hypothesis of the rational person.
The Finely Tuned Universe
The argument is made that if the Universe did not have the force relationships, fundamental structure, etc. that it has, the resultant universe would not be conducive to the emergence of complex structures, such as life. It has been a matter of great controversy with some scientists arguing quite clearly to a desired conclusion. Of course, Theists are also inclined to do so.
I would assess that the basic natural laws appear to result from intelligent design and, at least at this time, it is a far more plausible explanation than any of the alternatives. The aversion to include Intelligent Design as an explanation for the start of the Universe has led to, what I consider to be, a scientific embarrassment. Physicists are slowly moving away from the Copenhagen Interpretation of Quantum Mechanics toward the Many Worlds Interpretation, not because it is less problematical, its not, but because that by doing so they avoid the need to conclude that the Universe was intelligently designed.
This is, I believe, an effort to avoid the difficulties of the Strong Anthropic Principle. To explain this, suppose that you bought a lottery ticket and won the Jackpot. That someone was going to win it eventually, is a foregone conclusion. However, that you won it is likely to appear very, very improbable to you. We, collectively, are not at all surprised that someone won. This is equivalent to the Weak Anthropic Principle and does not argue for an intelligently designed Universe.
Now, however, suppose that you had the only lottery ticket and you won. In this case, we all are likely to think that something is hinky. The odds that you have won is no different - extremely remote. However, that the only ticket that existed won is not a certainty but, rather, is as improbable as it is that the winner was you.
The Finely Tuned Universe, when considered within the context of the Copenhagen Interpretation, leads to a situation similar to one where you win with the only lottery ticket sold. The Many Worlds Interpretation, on the other hand, is akin to the situation where millions of lottery tickets are sold and a winner is actually likely. The Weak Anthropic Principle basically says that we should not be surprised that we live in a Universe that is finely tuned because it is a requirement for us to be here thinking about it.
Remember that Physicists originally believed in a steady state universe. Einstein inserted a 'cosmological constant in order that his equations predicted one. They believe so, not because they had evidence, but because a 'big bang' Universe implied a moment of creation which smacked of intelligent design. It is amazing how, when the big bang was more or less proven, they blithely moved right past the idea of creation and without a shred of evidence assumed that a natural explanation for creation would be found.
They found one, of course, and it is non-trivial. They claim that 'nothing' is unstable and given enough time it will explosively turn into something. Surprisingly, the mathematics of quantum physics supports that conclusion, however, that interpretation creates other problems that is requiring Physicists to postulate that the 'universe' is actually just one bubble in a sea full of bubbles... Again getting them out of their Strong Anthropic mess.
There is a serious question under this interpretation as to whether the Big Bang was actually the beginning of the Universe. In other words, does a sea of quantum foam actually equate to nothing or is it actually a Universe with a net zero mass? This most surely begs the question of how long the quantum foam existed before it explosively turned into the plus sum mass Universe that we have now. It actually gets quite peculiar because it is precisely the rules of Quantum Physics that says that the quantum foam can spontaneously and explosively turn into something whose net mass is not zero on a universal scale. The likelihood of this happening is a probability function. In other words, given enough time it should happen.
So, we find ourselves with the next logical question. How did it come to be the case that the quantum foam existed and did with the necessary rules to cause the Big Bang to happen? In other words, while the 'non-divine' creation of the Universe appears to be supported, it really just 'kicks the can down the road.' Sooner or later, the issue of first cause will raise its ugly (to athiests) head.
In total, looking at cosmology and theoretical physics, the notion that the universe 'just happened' is not disprovable, but it is, well, a bit fishy. Intelligent design, while not provable, solves the problems efficiently and probably should be our working hypothesis solely on the basis of Occam's Razor. It has seriously been suggested that our Universe was created by 'aliens'. Scientists are, in essence, giving up and embracing Intelligent Design, but substitute 'alien' where Theists would put 'God.' Of course, as aliens, we quite reasonably wonder from where they came.
The First Self-Replicating Molecule
How did life begin? Or more precisely, how did the first self-replicating, mutation prone molecule come into existence? Evolution cannot provide the answer, since it requires replication to operate and, without such a molecule, evolution has nothing to work upon. Finding a mechanism for creating such a molecule has proven to be very, very difficult.
The leading candidate right now may be the polymerization of amino acids in suspension and left to dry on clays or crystals. Experimentally, we know that this leads to proteinoids and oligopeptides that, at least, give more reasonable building blocks than simple amino acids. To explain, in 1996 David Lee reported a self-replicating molecule of 32 amino acids. The specific sequence has the probability of forming randomly of 4^32 or 18,446,744,073,709,600,000:1 against. In other words, randomly, it just isn't going to happen. He created the self-replicating molecule, however, by combining two polypeptides of 17 and 15 amino acid chains. This changes the probability to 4^17+4^15 or 18,253,611,008:1 against or a billion times more likely.
This, then, leads us to an imagined scenario where a primordial soup splashes through tidal action upon volcanically heated rocks, slowly turning the primordial soup from one constitute of amino acids to one containing protenoids and oligopeptides. These compounds, in the quadrillions combine randomly in the sea until a self-replicating combination happens. The rest is evolutionary history.
This doesn't explain it all. It has been suggested that in order to sustain itself over a sufficiently extended period for evolution to take hold, these original cells would need to have a photosynthetic metabolism. Additionally, even if the absence of mitochondria, some method of metabolic processes would need to exist. Once again, we are stretching our credulity to accept that all of this could happen at once within one protocell.
Given the above, Intelligent Design does have a reasonable alternative. However, there are two caveats. First, where did these precise qualities of molecules come from and how reasonable is it that that characteristics of Carbon, water, Phosphorus and other compounds are such that they are capable of creating such a complex and self-sustaining system? It is a more fundamental and philosophical question that is reminiscent of the Finely Tuned Universe. We might call it the 'Finely Tuned Organic Chemistry' question. Second, the application of Occam's Razor does not really militate strongly for this abiogenisis hypothesis over the Intelligent Design hypothesis. Until we have it 'nailed down', the abiogenesis hypothesis is seems more than a little like a 'just so' story.
Another hypothesis that has found favor in the scientific community is the panspermia hypothesis. Quite simply it argues that the first self-replicating molecules blew in on the stellar wind. Or, conversely, it is hypothesized that an extra-solar body collided with the Earth and then, somehow, survived the trauma of impact and began replicating. Panspermia hypotheses have two serious problems. First, there is, so far, no plausible delivery mechanism. Second, it, too, kicks the can down the road. Where did these self-replicating molecules come from and how did they form there?
Recently it was suggested, seriously, that 'aliens did it.' Two problems with that. First, what, precisely is the difference between God and an Alien Creator? Second, where did the aliens come from? Again, the Intelligent Design can is being kicked down the road, not eliminated.
In the final analysis, we do not, at present, know how life began, either here or elsewhere. A naturalistic process is not unreasonable, though it suffers from the 'fine tuned organic chemistry' problem. Intelligent Design is and should be in the hopper of possible solutions, though characterizing them as aliens or God is unsupported and, frankly, not helpful. At present, Occam's Razor would appear to advise us to that some sort of intelligent and volitional agent interceded to reduce the improbability.
The Phyla and Class Problem
Defined as natural selection acting upon random mutations works well in explaining how species radiate within a genus and perhaps explains how genera emerge from within a family. However, it is ill-equipped to explain the Cambrian explosion of phyla and, most likely, the emergence of many Classes.
I first became aware of this problem with evolution in a Physical Anthropology book that was questioning how evolution could have resulted in bipedalism, if its survival advantage was increasing height in order to see over the savannah grass without a concomitant increase in size. In essence, there didn't seem to be any benefit to partial bipedalism, since it would be insufficient to provide the benefit of seeing over the grass. While there are several things wrong with this argument, it got me thinking about the problem of multiple mutations being required to provide the first increment of survival benefit.
I have had the most difficulty with birds and their modifications for the sake of flight. In order to accomplish the feat, bird must, 1) modify their presumed scales into feathers 2) redesign their bones to make them much lighter without sacrificing too much in strength, 3) reconfigure their front legs in such a way to allow them, with the feathers, to create a wind foil in the form of wings. Any one of these modifications does not seem to convey any survival benefit on their own. Only in combination do they allow for flight and its clear survival benefits, both as a predator and as a prey.
The problem is that flight is extraordinarily difficult for animals as big as birds. In other words, flight seems to require close to complete evolution to take place simultaneously in three separate genetic polymorphisms before any natural selection can act upon the genome. In fact, partial modifications would appear to be anti-survival. If there is a naturalistic explanation, it would appear that we would need to find a different evolutionary mechanism.
Might an intelligent and volitional agent have interceded to make these large jumps in evolution? It certainly is less problematical than any existing theory. Isaac Asimov once suggested that perhaps these large morphological changes are somehow implicit in the chemistry of DNA. Even if we were to accept that, again, we are just kicking the intelligent design can down the road. How likely is it that the chemistry of DNA would just happen to be such as to cause such dramatic and adaptive modifications to take place naturally. It suggests that the very structure of chemistry has been purposefully contrived so as to accommodate the needs of life.
The Lesson from Cellular Automata
In the 1940's Stanislaw Ulam and John von Neumann were the first to work with cellular automata. The are, essentially, a simple set of rules applied to a grid where the condition (visually black and white is the most common) of every square in the grid at t+1 is determined by the condition of its neighbors at t. Typically, these systems will have four rules, one for birth, one for death and one describing the initial state of the system.
In the 1970's they were popularized by John Horton Conway as 'The Game of Life'. For the past twenty years, Steven Wolfram has developed them and has reached a number of controversial conclusions. One of his research assistants, Matthew Cook, demonstrated that some sets of rules can be Turing Complete. The quick explanation is that the set of rules can be used to describe any desired state.
What this means is that some, far from all, sets of simple rules can lead to evolution, complexity and stability that is far from intuitively inherent in the rules. This is significant to Intelligent Design because it can be used to support Asimov's conjecture that the rules that govern DNA may have implicit in them complexities that are not clearly apparent. For example, some precursor organism suddenly and simultaneously developing wings, light bones and feathers may not be a random event. It may be implicit in the DNA itself.
Most dilettantes imagine that there is a long string of amino acids on the DNA molecule where the probability of a base pair substitution is about the same over the full length of the strand. This is not the case. While determining mutational rates at a particular gene site is very difficult, we have learned enough to know that, as an example, mutations in eye color are different than, say, the mutation rate for hair color. Also, the mutation rate for blue to brown, blue to green, brown to green, brown to blue, green to blue and green to brown are probably all different.
What this means is that between celluar automata and differential mutational rates, populations exposed to highly mutagenic environments may with a reasonable probability create organisms with a patterned suite of mutations. However, there is still something more than a little hinky about the notion that of all the possible mutational combinations, ones such as wings/light bones/feathers, should emerge. While providing a mechanism for phyla sized morphological differences to emerge, it would seem to suggest that the rules underlying mutation rates has been intelligently manipulated.
However, anyone who experiences the complex and apparently designed systems that can emerge in cellular automata is likely to be inclined to accept that such a complex system of mutations, as suggested by Asimov, may be inherent in the chemistry of DNA.
So, as should be the case in unsettled scientific questions, there are reasons to favor either a naturalistic universe or a intelligently designed one. However, on balance, intelligent design is substantially less complex that the purely naturalistic universe. While carbon based complexity may be inherent in the laws of the universe, the structure of those laws stretches one's credulity as a natural phenomenon.
Consequently, as a working hypothesis, I am a Deist. In other words, I operate on the assumption that the Universe is the result of intelligent volition, but I do not assume that the creator(s) have any particular interest in me or humanity in general. I do not even assume that the creator(s) even still exists. It is often stated that the assertion of Intelligent Design is not scientific because it is not amenable to verification. Actually, that is a bit of a red herring. That the Universe is a product of natural processes is also not amenable to verification. Yet it is a foundational assertion of science.
Actually, it is not necessarily the case for either intelligent design or naturalism that they are not subject to verification. We are not likely to find direct experimental evidence for either. However, it is not the only route to truth. Proof through reductio ad absurdum is an acceptable scientific approach. Both positions could be amenable to it. The more we know about the Universe the more likely that a disproof of one will surface. Since either the Universe was volitionally created or it wasn't, the disproof of one serves as a proof of the other.
It is ill-advised for advocates of Intelligent Design to militate for its teaching in schools, although something like the above could fall legitimately within the purview of a Philosophy of Science section. Absent that, teaching evolution without mention to the problems it has as a universal explainer of life or teaching Physics without introducing the student to the problem of creation, is irresponsible. The Mediocracy generally believes in naturalism, generally and evolution, specifically, as such and that is why it is difficult to change the curriculum.
Here is a logical peculiarity in our science curriculum. If a teacher were to mention all the possible explanations for the emergence of life and included in that, 'aliens did it', the teacher would be in no trouble. However, 'aliens' are just one of several possible intelligent designers. Logically, they fall within that proscribed category of explanation. What we have here is not scientific principles. What we have is an animus of the educational system toward religion and by extension any explanation that would not categorically preclude a God.
Anyway, I titled this essay, 'Rational Intelligent Design' and I believe that I have successfully defended my position that Intelligent Design is the most rational working hypothesis in answer to several open scientific questions. There is a very strong tendency within the Liberal Culture to characterize adherents of Intelligent Design as universally ignorant and stupid. I am profoundly not either and I hope that disproves that offensive little piece of ad hominem.