1. Why do the genomes of salamanders have 50 times more DNA than humans?
When genes were first discovered, it was commonly thought that humans, appearing to be the most "complex" organism, would be the most complex at the genetic level, too. But that is not so. Humans are less complex, genetically, than many other "simpler" creatures. We humans need to stop looking at characteristics such as intelligence as somehow evolving from a less-complex state to a more-complex state. Complex traits such as intelligence, instinctive reactions, or the makeup of complex organs such as the an eye or feather are no more complex, at the genetic level, than any other trait or organ -- it's just a bunch of genes.
Dr. Senapathy says genomes came about through random assembly of genetic material (including reused genes and new genes). If that is so, you would expect the amount of DNA in genomes to vary, and somewhat independently of any in-pond relatedness. Large chunks of DNA, mostly junk, could be included, while other chucks are removed. The end result need only survive and reproduce. Also, the chances of getting a "complex" organism (e.g. humans) is the same as getting a less complex organism (e.g., a worm) because the amount of DNA is not related to our expressed complexity.
2. Why do supposedly related organisms have widely varying amounts of junk DNA (the C-value paradox)?
If you look at the amount of DNA in various organisms, you will find wide variations between "distant" and even among "close" creatures. If evolution was the cause of all these various organisms, you would expect the amount of DNA to track the various relationships between supposedly related organisms. Why should a huge amount of DNA suddenly be added or removed along the lines of descent? This is the "C-value paradox," and is discussed in the book. Dr. Senapathy's theory easily explains (and predicts) this wide variation.
3. How can complicated new body parts or new organs (e.g., eyes and feathers) form when the necessary thousands or millions of intermediate steps would have offered no selective advantage?
New genes and combinations of new genes were randomly assembled in the primordial pond. If a particular combination of genes resulted in a creature that could survive and reproduce, it could easily have a different set of organs from other organisms because of the unique genes chosen from the pond.
4. How could those many steps needed to form new body parts occur in the relatively short time during which those new organs and organisms were coming into existence?
It didn't happen in many steps. Although some organs could appear to come about in a step-wise fashion through some genetic reuse over many new seed cells, some organs could have formed from the genes randomly chosen from the pond. Unlike evolutionary theory, a sequence of many steps and the selection of favorable mutations along the way are not required to go from one organism to another.
5. How could all the hundreds of proteins needed for vertebrate blood suddenly come into existence at the same time from invertebrate "blood," when none of those proteins are present or useful in any invertebrate?
Until the "correct" combination of randomly assembled genes were chosen that were able to code for all of the proteins needed for vertebrate blood, no vertebrates were born. Once the random assembly resulted in the first viable vertebrate, the DNA from that successful organism would be multiplied (through growth and reproduction) and many more copies of the genome would be available for reuse to form other vertebrates. Over millions of trials, most of which would result in failures (non-viable organisms) some resulted in viable creatures.
6. How could so many unique creatures suddenly appear over a short time 500 million years ago, but practically no new creatures appear since (the Cambrian explosion)?
The rate of formation of new species is a function of the productivity of the primordial pond. Once it became productive, many new viable creatures would have formed in a relatively short time. The pond would have stopped being productive when it ran out of DNA material or when environmental conditions changed enough the affect the pond chemistries.
7. If the mutation rate is constant, why has the rate of "evolution" slowed down so much since the Cambrian explosion?
Mutations are not responsible for the wide variety of organisms. Mutations do not result in distinct, new organisms. Mutations either result in slight modifications, variations, and similar species or the mutations result in disaster.
8. What accounts for the wild and unique creatures of the Burgess Shale?
It was a separate pond, at least for some period of time. During the time the Burgess Shale pond was productive, the creatures it produced were randomly assembled in ways different from the other primordial ponds. Randomly-assembled unique genes and the genomes available for reuse resulted in a different set of independently-born organisms.
9. If life happened once (it did, right?), then why not twice? Or a hundred times? Or a million, or a billion?
It did happen many millions of times.