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It is mentioned early in the movie, that dinosaurs are more similar to birds than to reptiles. So at least in movie continuity, this is true as in reality. So why then wouldn't they use bird DNA instead of amphibian DNA?
In-universe explanations only please, please - I know the plot needed an excuse for the spontaneous sex-changing.
This is from memory and it's been a while since I've read the book and it is mostly mentioned there rather than the film but there are a number of relevant points linked together to form a vital plot point.
We can deduce from their success that the scientists must have found a way to succeed. In addition, and remembering that the book was written in the late 80s when the understanding of genetics was considerably less than nowadays, the science in Jurassic Park is not viable in the real world so we can also assume that genetics is less difficult to get working right. It's also viable to assume that the scientists experimented with several different theories before they found the one that worked. Using frog DNA was just the first theory that worked.
Dinosaur DNA is not complete so it must be 'filled in' with other DNA. Most of the DNA that makes up a genome is either 'junk' (we don't know what it does) or common (shared by different species). Frogs are amphibians which evolved before dinosaurs, therefore using their common or junk DNA would likely be a better fit than using lizard or mammalian DNA.
Certain frogs apparently have the ability to change their gender. Thus when the scientists used 'junk' Frog DNA to make dinosaurs it accidentally gave the dinosaurs the ability to change gender. This allowed the dinosaurs to breed which is revealed firstly when Grants finds a Velociraptor shell and then when Malcolm demonstrates a flaw in how the park measures populations of dinosaurs, thus justifying Malcolm's saying that 'nature finds a way'.
Not entirely sure whether they knew this info or not when Jurassic park was set or not, but presumably if they are lifting genetic material from frogs they should know the size of the genome.
The mean sizes for frogs vs birds genome is 4.68pg ± 0.13 (pg is picograms of genetic material for one complete copy of the genome) vs 1.38pg ± 0.01, meaning that the frog genetic code has about 3 times as much data. They may have felt the extra genetic material would make it easier for them to find DNA that corresponds more closely to the dinosaur DNA better.
Keep in mind that having more genetic data in the genome doesn't always make an organism more complex, it may just mean that the organism hasn't "cleaned" it genetic code and there is a lot of older left-over material from the process of evolution.
The sizes of the genomes are from Gregory, T.R. (2005). Animal Genome Size Database. http://www.genomesize.com
Another fun factoid is that the largest frog genome is 13.40pg, Ceratophrys ornata (8n), Ornate horned frog while the largest bird genome is 2.16pg, Struthio camelus, Ostrich. This means the largest genome from the frog is ~6 times as large as the largest bird genome.
I know its kinda complicated, but I hope it helps.
Also from http://www.genomesize.com/statistics.php?stats=amphibs#stats_top you can see that amphibians other then frogs can have a significantly larger genome then just frogs, they may have just settled on frogs because they are a more easily managed genome then the Gulf coast waterdog, for example, with a genome of 120.60pg (9 times the size of the largest frog).
First some background reading on Henry Wu's worldview. Page 123 in my copy:
[Wu] paced the living room, pointed to the monitors. "I don't think we should kid ourselves. We haven't re-created the past here. The past is gone. It can never be re-created. What we've done is reconstruct the part — or at least a version of the past. And I'm saying we can make a better version."
"Better than real?"
"Why not?" Wu said. "After all, these animals are already modified. We've inserted genes to make them patentable, and to make them lysine dependent. And we've done everything we can to promote growth, and accelerate development into adulthood."
Hammond shrugged. "That was inevitable. We didn't want to wait. We have investors to consider."
"Of course. But I'm just saying, why stop there? Why not push ahead to make exactly the kind of dinosaur that we'd like to see? One that is more acceptable to visitors, and one that is easier for us to handle? A slower, more docile version for our park?"
Hammond frowned. "But then the dinosaurs wouldn't be real."
"But they're not real now," Wu said. "That's what I'm trying to tell you. There isn't any reality here." He shrugged helplessly. He could see he wasn't getting through. Hammond had never been interested in technical details, and the essence of the argument was technical. How could he explain to Hammond about the reality of DNA dropouts, the patches, the gaps in the sequence that Wu had been obliged to fill in, making the best guesses he could, but still, making guesses. The DNA of the dinosaurs was like old photographs that had been retouched, basically the same as the original but in some places repaired and clarified, and as a result— [...]
With that in mind, here's page 208 in my copy (just a little more than halfway through the book), some time after Grant has first brought up the idea of frog DNA being relevant:
[Wu] still wasn't clear about why Grant thought frog DNA was important. Wu himself didn't often distinguish one kind of DNA from another. After all, most DNA in living creatures was exactly the same. DNA was an incredibly ancient substance. Human beings, walking around in the streets of the modern world, bouncing their pink new babies, hardly stopped to think that the substance at the center of it all — the substance that began the dance of life — was a chemical almost as old as the earth itself. The DNA molecule was so old that its evolution had essentially finished more than two billion years ago. There had been little new since that time. Just a few recent combinations of the old genes — and not much of that.
When you compared the DNA of man and the DNA of a lowly bacterium, you found that only about 10 percent of the strands were different. This innate conservatism of DNA emboldened Wu to use whatever DNA he wished. In making his dinosaurs, Wu had manipulated the DNA as a sculptor might clay or marble. He had created freely.
[Wu runs a computer search for Rana DNA among the dinosaurs.]
The result was clear: all breeding dinosaurs incorporated rana, or frog, DNA. None of the other animals did. Wu still did not understand why this had caused them to breed. But he could no longer deny that Grant was right. The dinosaurs were breeding.
So to answer your question directly (in-universe, in Henry Wu's worldview): sure, "dinosaurs are more similar to birds than to reptiles" in body shape and whatnot, but this is just an artifact of the human-scale world. At the molecular level, it simply doesn't matter to Wu where the DNA comes from, as long as it looks about right and makes the thing work like it should. One molecule is just as good as another. Insisting that each snippet of DNA come "originally" from an animal that's close to dinosaurs on the archaic Tree of Life is just as ridiculous as insisting that the H2O you drink come "originally" from an artesian aquifer in Viti Levu. It's just molecules, people! They're not magic.
(So much so that when frog DNA does turn out to be the key, Wu is completely baffled. He immediately accepts the evidence in front of him, but cannot even guess at an explanation. His philosophy is turned completely upside down — he is confronted, after all, with magic.)
Out-of-universe, I don't know whether many biologists would subscribe to Wu's view about the interchangeability of DNA fragments. To me it seems plausible, but it's certainly also caricatured to make a point. Wu's arrogant reductionism is part of his tragic flaw just as much as John Hammond's childlike idealism is part of his.
There might be some-pseudo scientific explanations that could fit the bill.
