At the request of others I’m reproducing a recent comment as an article.
UD member Fross writes:
I understand that the ID position is that the protein itself had to have been designed, not the variations that can occur through mutation.
Proteins donÃ¢â‚¬â„¢t automatically warrant a design inference. It depends on the function of the protein and interdependencies on other proteins. A signalling protein could easily get a random mutation that slightly modifies a biologically active site making it more or less able to bind with a target and that can change a whole downstream cascade of events with large scale ramifications. I think I read recently that such a site has been implicated in whether a dog turns out to be a large or small breed, for example, as the cascade result is how much growth hormone is produced. ItÃ¢â‚¬â„¢s not the sole determinant though as you can cross a large breed sire with a small breed bitch and the puppies never turn out so large the mother canÃ¢â‚¬â„¢t bear them.
On the other hand some proteins that are components in intricate molecular machines and because their shape must critically match the shapes of other components for the machine to function variations that change the shape would cause the machine to not work without simultaneous variations that change the shape in other proteins. These simultaneous changes seem to go far beyond any reasonable odds of happening together. Click on the Ã¢â‚¬Å“CategoriesÃ¢â‚¬Â sidebar Molecular Animations to see some examples of this type of molecular machinery. People have found this one particularly compelling for its simplicity, ease of understanding, and difficulty in imagining how it could have evolved ex nihilo. The problem it solves is DNA supercoiling which must have been a problem from the very first DNA molecule, all forms of life have one or both these machines in them, so it presents a classic chicken/egg problem with only one protein involved. What came first, the DNA molecule that has to have a topoisomerase family enzyme in order to be unwound for replication and reading or the DNA molecule that carries the information required to construct a topoisomerase enzyme? And this is a very very simple machine made of a single protein unlike many others youÃ¢â‚¬â„¢ll see in that animation series in which the machines are formed of multiple proteins. A ribosome in particular is composed of many different proteins and ribonucleic acids working together. The whole machine must be assembled and working in order produce the parts that make the up machine that makes the parts! This particular machine is also present in every form of life and is so basic (itÃ¢â‚¬â„¢s the machine that reads the coded information in a gene and builds a protein according to the coded assembly sequence) no life as we know it is possible at all without it. HowÃ¢â‚¬â„¢d that happen without a designer envisioning the entire machine in abstract then building all the hundreds of interlocking pieces that make it up simultaneously? ItÃ¢â‚¬â„¢s like proposing that you can build an automobile by starting off with randomly shaped chunks of metal and just randomly changing the shapes until they all fit together into a working automobile. To compound the problem you need a fully working automobile to gather the parts together to make an automobile. This is the story the chance & necessity pundits ask you to accept and take as a matter of materialistic faith that, impossible as it sounds, eventually science will reveal how it was done without intelligent agency.
And speaking of dogs, that brings up what appear to be fundamental limits on variation that mutation and selection can produce. Dogs are possibly the most widely varying species on the planet while still remaining a single species. In 20,000 years of artificial selection and preservation of variants that never would have survived in the wild there hasnÃ¢â‚¬â„¢t been a single variant with an anatomical feature not characteristic of canines nor has a new species of dog emerged. Not even something as simple as a retractable claw. The variations are entirely limited to the deleterious (dogs are predisposed to a large litany of genetic disorders) and the cosmetic. You can get big dogs and small dogs (change in scale) you can get wide variation in ratio of body part size (change in aspect), you can get broadly different coloration, patterning, coat length and thickness, and thatÃ¢â‚¬â„¢s about it. What artificial selection and preservation canÃ¢â‚¬â„¢t accomplish seems to be even farther beyond the scope of natural selection and preservation which is restricted in that any variation must be either nearly neutral or decidedly beneficial in order to have the selection value required to fix the variation within the population.
Island species are another good example of these limits. Isolation on an island for millions of years and the quite different environmental pressures (or lack thereof) drives selection at an accelerated rate for island species. The result is often dwarfism or gigantism but never any variation on the level required for evolution writ large like the appearance of a novel cell type, tissue type, organ, or body plan. In short, the observed limits of highly accelerated natural selection over millions of years are same kind of limits in variation you see in dogs through thousands of years of artificial selection but nothing beyond that. It appears there is something other than random mutation and natural selection that produces the fundamental differences between the higher taxonomic categories.
Intelligent agency solves all these problems. We already know for a fact that intelligent agency with the capability or near capability of building or modifying complex organic machines in defiance of impossible odds of random assembly is extant in the present universe. That agency is us. The question then becomes one of how many such agencies exist in the universe, what forms they can take, did any of those possible forms predate humanity, and did they have the physical means, motive, and opportunity to accomplish the things we see here without violation of any known laws of physics. For example any agency in a remote galaxy would be prohibited from influencing anything in this galaxy because of the limitation imposed by the speed of light barrier. Given that normal matter and energy compose only a small fraction (5%) of what makes up the universe it seems premature to rule out exotic forms of intelligent agency that could very well be composed of non-baryonic matter that we only suspect exists through indirect observation of its gravitational effects on normal matter. In fact what we consider normal matter and energy may be the minority component and thus really an atypical form in the big picture – the froth on the top of an unplumbed ocean. Hubris is rampant in the halls of science today. Of course thatÃ¢â‚¬â„¢s nothing new. The history of science is littered with disgarded theories that were once thought to be writ in granite. Thinking we have a fundamental understanding of nature where that understanding is lacking only in the fine details is something that has plagued inquiry since the getgo.