But it goes a great deal deeper than that. We know how DNA consists of coded blueprints to help replicate all the proteins found in an organism (not to mention a lot of other proteins found only in the organism’s ancestors). But where is the information on how these proteins are then assembled into cells, tissues, organs and organ systems? Sure we can catalog all the materials in a house, such as framing, nails, pipes, wires, bricks, tiles, glues, paints, plaster, drywall, cement and so on. But that doesn’t tell us how they are shaped and assembled in order to finish the completed structure. If all the materials to build a house were available at Home Depot, you’d still need several craftsmen’s skills to bring them together, in the right order, to build a house. That information is not stored in the list of supplies you take with you to pick up the construction material.

We are not just undifferentiated piles of proteins, we are put together in a certain sequence, over a long period of time (that’s what embryology is all about). Where is the information for how to construct a human in the womb stored? I understand it may be coded somehow in the secondary and tertiary structure of DNA, but nobody really knows for sure. BTW, “secondary and tertiary structure”, (and there may be other levels) refers to the contortions and shape the DNA contorts itself into. The primary structure is the double helix itself, we have a pretty good understanding of that. But that double helix twists itself pretzel-like into higher order morphologies…

And consider this, the DNA not only codes up the design of the adult organism (with variations), but it also communicates the structure of that life-form at different stages in its life. Invertebrate DNA also must know the anatomy and physiology of the egg, larvae, pupae and adult stages of the animal, which may be quite different, each magnificently adapted to totally differnt environments and ecological niches. How the hell does something like that evolve just by a purely stochastic process like natural selection? Some species have alternate lifestyles, popping back and forth between to very dissimilar organisms; some coelenterates alternate between a polyp and medusa body plan, and the common fern alternates between two totally different types of
architecture. Sponges, on the other hand, have many different types of cells and tissues, but no organs as we know them. Still, somehow they manage to organize themselves into recognizable shapes. Some creatures, like the Portuguese man-o-war, aren’t even organisms per se, they are colonies of specialized individual animals which cannot exist independently. And for some real weirdness, read up on the life cycles of slime molds.

In social insects, the anatomy and physiology of each caste (worker, nurse, warrior, queen, drone) must be coded separately in the DNA, plus the instructions to trigger the desired form by simply altering the diet of the larvae. How did that evolve from a pruning selective process like our snow-dwelling furry critter?

I think there is a hell of lot going on that we don’t understand, and I don’t think some puerile hypotheses like Creationism or “intelligent design” can ever hope to explain any of it any more than “natural selection” can. There is something going on, some kind of information processing at the cellular and molecular level that is truly wonderful.

Random variations will operate on one characteristic, making it approach some ideal because selection will prune out the bad variants. But what if you need two characteristics, like white fur AND fatty deposits under the skin? How much longer will that take? What about three, what about a thousand? A million? How will the simultaneous development of all these independent characteristics be coordinated? How will they be managed and optimized to work together? How are they integrated so the life form evolves rather than get tangled up in its own infinite contradictory possibilities?

I think intelligence is involved. Not intelligence from a supreme being, but an intelligence which somehow arises spontaneously in the complexity of biochemistry. I think DNA computes. It calculates. It processes data and rigs the odds in its favor. I believe DNA (and its associated accessory compounds) is capable of thought. Not thought in the way we think of it, but thought nonetheless. It analyzes data, makes decisions, learns from its mistakes, follows up on promising ideas. Its alive. And it is busy making and perfecting even better thinking machines to help ensure its own survival and propagation.

Domesticated animals of widely different species seem to share some common traits: changes in body size, in fur coloration, in the timing of the reproductive cycle. Their hair or fur becomes wavy or curly; they have floppy ears and shortened or curly tails. Even Darwin noted, in On the Origin of Species, that “not a single domestic animal can be named which has not, in some country, drooping ears.” Drooping ears is a feature that does not ever occur in the wild, except for in elephants. And domesticated animals possess characteristic changes in behavior compared with their wild brethren, such as a willingness or even an eagerness to hang out with humans.
…
Starting at one month of age, and continuing every month throughout infancy, the foxes were tested for their reactions to an experimenter. The experimenter would attempt to pet and handle the fox while offering it food. In addition, the experimenters noted whether the foxes preferred to hang out with other foxes, or with humans.
Then, upon reaching sexual maturity (seven to eight months), they had their final test and assigned an overall tameness score. They rated each fox’s tendency to approach an experimenter standing at the front of its home pen, as well as each fox’s tendency to bite the experimenters when they tried to touch it. Only those foxes that were least fearful and least aggressive were chosen for breeding. In each successive generation, less than 20 percent of individuals were allowed to breed.
…
The domesticated foxes were more eager to hang out with humans, whimpered to attract attention, and sniffed and licked their caretakers. They wagged their tails when they were happy or excited. (Does that sound at all like your pet dog?) Further, their fear response to new people or objects was reduced, and they were more eager to explore new situations. Many of the domesticated foxes had floppy ears, short or curly tails, extended reproductive seasons, changes in fur coloration, and changes in the shape of their skulls, jaws, and teeth. They also lost their “musky fox smell.”

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763232/
You might want to look into epigenetics- it seems that DNA can take your recent ancestor’s experiences into account when expressing itself in you… not intelligence of course, but a clever way of approximating the best strategy for survival.

http://discovermagazine.com/2013/may/13-grandmas-experiences-leave-epigenetic-mark-on-your-genes

http://io9.gizmodo.com/how-an-1836-famine-altered-the-genes-of-children-born-d-1200001177

Among the 1905 birth cohort, those who were grandsons of Överkalix boys who had experienced a “feast” season when they were just pre-puberty—a time when sperm cells are maturing—died on average six years earlier than the grandsons of Överkalix boys who had been exposed to a famine season during the same pre-puberty window, and often of diabetes. When a statistical model controlled for socioeconomic factors, the difference in lifespan became 32 years, all dependent simply on whether a boy’s grandfather had experienced one single season of starvation or gluttony just before puberty. It appeared that Överkalix grandfathers were somehow passing down brief but important childhood experiences to their grandsons. Bygren knew that such a suggestion would be received by some of his peers as scientific treason. DNA sequences are passed down, experiences, after all, are supposed to die with the individual. Still, the longevity findings in Överkalix were so consistent and pronounced that Bygren and two colleagues began submitting them to scientific journals. But it would be over a decade before the report appeared.