Pyramids are not self replicating organisms. Pyramids do not create new pyramids. The same is true for a watch. My watch has never self replicated itself yet. Life is the opposite of your example. Life does reproduce and pass on characteristics. The genetic material inside life can recombine, change, transfer genetic material, and we now have epigenetic factors to stabilize some sections of critical dna and increase the variability of other sections of dna. Just look at the variations in humans - not designed but generated from vast variability of our genetics. As for the gaps closing - there are new fossils being found as well as new understanding of genetics all of the time.
On a quick search I found this from the University of Cork.
"A team led by researchers from University College Cork analysed the chemical composition of melanosomes extracted from internal tissues, including the heart, liver and lung, of a range of existing and fossilized animals. They found that each organ had a distinct signature in its metal content, suggesting that melanosomes also manage metal metabolism around the body.
These chemical signatures are preserved in fossils, which will enable researchers to reconstruct the internal anatomy of extinct species. In a Libros tadpole fossil, for example, a region rich in titanium and copper reveals the liver’s location."
There is an example. Yes it is just of piece of evidence and not the entire explanation but that is how science works.