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Consider how an octopus looks at a rock and it's entire body blends in to resemble the rock. Consider how insects evolved to resemble leaves or twigs. Even frogs, butterflies and other creatures evolved similarly. When the Pakiectus slowly evolved into the dolphin, there would have been a conscious observation made by the creature, that it could swim better if it had appendages similar to the fishes it saw around it. Or, it could have simply been a realization of how it was able to push water better, when its phalanges were held together tightly. Consider how the nostrils of the whale and dolphin moved to the top of the body. Or even the transition from fins to limbs. In blind cave fishes, 'master switch' genes triggered their blindness. Perhaps light signals are required to keep such genes active. Finch beak sizes evolving rapidly, were theorized as an extra-genetic mechanism (epigenetic changes, that are independent of changes in the DNA sequence).

For the body to evolve a specific type of adaptation, there has to be some kind of knowledge within the cells or the neural network, about which specific part of the DNA to alter or silence, in order that the progeny would have a certain specific type of an altered body shape or function. Even if there's no specific knowledge, there could be a trial and error way of slightly tweaking some known part of the DNA to try and achieve the desired change in body structure or function. Or, the imagination of the creature would have some way of expressing a desire for what kind of change it wants to achieve, and that conveys a signal to perhaps a stem cell that's capable of 'visualizing' and altering cell structure and function. For this, the cells or body would need some kind of a database and 'thinking' function which can bring about such specific changes.

Is there some kind of a "research and development department" in certain cells or a network of cells, which allow it to observe the cause-and-effect of various molecular interactions, and allows it to design molecular and bodily architectures? I would assume that such mechanisms would be capable of manufacturing specific types of molecules. How else would Conus geographus know how to use insulin to disable fish? How else would sea creatures figure out that they could use the oxygen from air to adapt to become land creatures? How else would snakes evolve venom, and termites evolve enzymes to digest wood? How were redox centers designed to allow electrons to jump in a specific direction (3:48 of the video), and how were the F1 F0 ATP synthase designed like a motor and 'placed' at a specific point in the cell to perform a specific function?

There has to be some kind of programming or intelligence outside the DNA, which allows a broader scale visualization of the environment and the body. The intelligence takes decisions based on that. Axon guidance proteins are one such example, where a precise decision is taken for neural connectivity in a jungle of neurons. Could such intelligence be a part of the cytoplasm (because I've only known of cells being created from cells, but never independently appearing into existence. Even viruses need cells to replicate)? Is there any current knowledge that provides pointers regarding this?

ps: Before 1982, conventional thinking was that bacteria couldn't survive in the stomach's acidic environment. But H.Pylori did, and was discovered. Louis Pasteur speculated that rabies could be caused by an extremely small pathogen. Later, viruses were discovered. Cholera was discovered by the initial inference that brewery workers weren't contracting cholera. This process of questioning and inference is what takes science forward. Please don't stomp down my questions just because it does not fit the current hypothesis of mutations. If anything, you should agree that the scientific community is yet to discover a lot more intricacies about cellular function.

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    – Bryan Krause
    Commented May 13 at 2:15

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The short answer, is that there is no current knowledge of any coding or intelligence outside the DNA.

The long answer (see chat) is that some scientists speculate on cellular intelligence and the ability of the network of individual entities to store memory via the network (see this, this, this, this, this and this. Plus a wiki for some other references). However, as per current knowledge, a cell just follows the "instructions" it's given in the transcribed portion of its DNA. There is some study ongoing regarding epigenetic changes which may influence evolution too (changes in gene function and expression patterns that are independent of mutations in a gene’s DNA sequence, yet these changes may still be inherited).

[community members: please feel free to edit this answer if you feel any information is lacking]

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