hey, a very nice analogy, too bad it doesn't apply to evolution.
"Common sense" is not applicable in almost all of science. The evidence is. And it's perhaps important to remember that "fish" and "bird" are relatively arbitrary* boxes drawn around what amounts to a spectrum. A fish will always give birth to a fish, but to a slightly different fish, and eventually those differences add up. If you were to view the entire evolution of dinosaurs in real time (imagine, for the moment, that you are immortal), you could go from early theropods to modern seagulls and at no point would you look and say, "that's no longer a dinosaur", but if you were given an early therapod and a modern bird, you could easily draw some boxes. Make sense?
*There are non-arbitrary characteristics, but how the boxes are drawn and what characteristics are chosen are, to a certain extent, arbitrary. To make this clear, if you look at this image:
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You could say that red stops at "actually", at "purple", or at "tiny changes", and it would be hard to claim that any is more valid than the last. That's what I mean by "arbitrary". When we draw a box between "humans" and "non-human apes", we have a similar difficulty determining what in the fossil record can count as each.
again from koonin:
The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the Tree of Life as we knew it but also another central tenet of the Modern Synthesis inherited from Darwin, gradualism. In a world dominated by HGT, gene duplication, gene loss, and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.
Equally outdated is the (neo)Darwinian notion of the adaptive nature of evolution: clearly, genomes show very little if any signs of optimal design, and random drift constrained by purifying in all likelihood contributes (much) more to genome evolution than Darwinian selection 16, 17. And, with pan-adaptationism, gone forever is the notion of evolutionary progress that undoubtedly is central to the traditional evolutionary thinking, even if this is not always made explicit.
The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution (Box 1). So, not to mince words, the Modern Synthesis is gone.
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