Asking for scientific 'proof' is essentially asking for the impossible. Scientists do not really prove things, they examine evidence and compare competing hypotheses and models. It would be more accurate to say that scientists disprove ideas that are shown to be wrong by the data. With this in mind I would like to discuss evidence.
Let us consider cetaceans, such as whales, dolphins, and porpoises that live in the water. However, they are mammals and so common descent proposes that in order for them to be related to other mammals cetaceans must ultimately be descended from land mammals. Now when we look at the fossil record we see a whole series of temporally arranged fossils appearing to document the evolution of whales from a land mammal; Indohyus, Pakicetus, Ambulocetus, Dalanistes, Maiacetus, Rodhocetus, Takracetus, Gaviocetus, Basilosaurus, Dorudon, Mysticetes, Odontocetes. These fossils demonstrate everything we would expect to see; such as progressive loss of hind limbs, and the gradual migration of nostrils back towards the top of the head to forum a blowhole. This is not Ã¢â‚¬ËœproofÃ¢â‚¬â„¢ of anything, but it is reasonably compelling and suggestive of a macroevolutionary transition. Remember also that nobody is proposing that these organisms are a direct line of ancestors and descendants. They simply represent an overall picture; orginally in the fossil record there are no cetaceans at all, and then we see a gradual series each appearing to be slightly less like a land-based mammal, and progressively more like a modern whale.
Now not only is that the case, but we also observe the same processes at work during their embryological development. Cetaceans develop hindlimb buds at the exact same stage of their development as other mammals, and these are essentially indistinguishable from those in other mammals at that stage. In cetaceans, the buds later regress back. Cetacean nostrils develop of the tip of their nose but then migrate and fuse into a blowhole on the top of their head. Thus we see a remarkable convergence between fossils and embryological development. Again, not Ã¢â‚¬ËœproofÃ¢â‚¬â„¢, but we do have converging lines of evidence pointing towards the same conclusion.
Of course, nowadays we are able to sequence genomes and look at organismsÃ¢â‚¬â„¢ genes. When we look at the genomes of cetaceans we find that they have the remnants of genes for land-based olfaction and vision, as well as remnants of genes for making hindlimbs.
All of this data is explained very well by common descent and coheres together to make a compelling case. It does not mean we have 'proven' that cetaceans are descended from land-mammals but it is certainly something that is very well supported by the data.
'proof' Vs Evidence
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