Exposing the evolution theory. Part 2

Using a phylogeny based on evolutionary distance and known sequences from living species you can reconstruct the ancestral sequence. If an enzyme has a new function, then it isn't broken. It still has function.

My language has been the same from start to finish, and I still have not seen you put Corvettes into a nested hierarchy as we do with species. If life evolved then they should fall into a nested hierarchy based on shared derived features. That has been the argument for evolution since the mid-1800's. The fact that designed things do not fall into a nested hierarchy when organized by shared derived features demonstrates why this evidence points to evolution and not to intelligent design. The lines represent groups, and where they meet represents a group of shared derived features. Phylogenetic signal does not assume evolution. It is a measure of how well the distribution of characteristics matches a tree-like structure. If you randomly assign characteristics to a set of hypothetical species then it will return a low phylogenetic signal. It is a measurement, not an assumption.

We all miss RAZD. It's nice to see his words still having an impact. Notice how there are groups within groups in the diagram? That's a nested hierarchy, also known as the tree of life. In eukaryotes, the vast, vast majority of characteristics are inherited vertically, so up the branches of the tree. Notice how the evolution of a characteristic is transmitted up the branches of the tree above.Look at where hair evolved. This means that hair could not be transmitted to birds because it did not evolve on a branch below birds.Evolution and common ancestry perfectly explain why we see this tree-shaped pattern, and the confirmation is example after example of this pattern in both shared and derived characteristics and in the divergence of DNA.

Flight isn't a physical characteristic. If you look at the different adaptations for flight you will see that those adaptations stay within a tree-like structure. For example:Those are two different limbs, and they stay within each of their branches of the tree of life. You don't see any birds with a bat-like wing, and you don't see any bats with a bird-like wing. You don't see any bats with flow through lungs, and you don't see any birds with tidal lungs. You don't see any birds with hair, and you don't see any bats with feathers. There are no cross-overs of flight adaptations. Because evolution only has to be better than the competitors. This wouldn't be the case if life was separately created by an all knowing and all powerful deity.

Why would denser bones prevent bats from having a bird-like wing? Why wouldn't a bird-like wing be well suited to the bat physique? Why couldn't bats have feathers? Why couldn't bats have flow through lungs? Why couldn't birds have teats to feed their young? Why can't bats lay eggs with calcified shells? No, it isn't I who has the misunderstanding. Humans regularly design organisms that violate a nested hierarchy, and they are perfectly fine. Humans regularly replace mouse genes with human genes in research settings, as one example. Human designs like cars, bicycles, and planes don't fall into a nested hierarchy. There is absolutely no reason why life should fall into a nested hierarchy if species/kinds were separately created.

Yes, it is. Then why do bats have denser bones? Why didn't the designer give them lighter bones? No, we wouldn't. They would still have other mammal features like three middle ear bones, cusped cheek teeth, etc. They would have a mixture of mammal and bird features. So why don't we see any? Why don't we see the billions of possible combinations of features that would violate a nested hierarchy? Why do we only see one pattern out of billions that evolution would produce?

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Now, since the days of Linnæus this principle has been carefully followed, and it is by its aid that the tree-like system of classification has been established. No one, even long before Darwin's days, ever dreamed of doubting that this system is in reality, what it always has been in name, a natural system. What, then, is the inference we are to draw from it? An evolutionist answers, that it is just such a system as his theory of descent would lead him to expect as a natural system. For this tree-like system is as clear an expression as anything could be of the fact that all species are bound together by the ties of genetic relationship. If all species were separately created, it is almost incredible that we should everywhere observe this progressive shading off of characters common to larger groups, into more and more specialized characters distinctive only of smaller and smaller groups. At any rate, to say the least, the law of parsimony forbids us to ascribe such effects to a supernatural cause, acting in so whimsical a manner, when the effects are precisely what we should expect to follow from the action of a highly probable natural cause.
--George Romanes, "The Scientific Evidences of Organic Evolution", 1882

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Why can't humans have the eyesight of a hawk and the smelling ability of dogs? These aren't even optimal, and yet humans don't have them. Why?Why does 90% of our genome accumulate mutations at a rate consistent with neutral drift? I suspect that you would reject any and all evidence, no matter how significant it is.What features would a fossil need in order for you to accept it as being transitional between humans and a common ancestor shared with other apes?What pattern of similarities or differences in genomes would you accept as evidence for shared ancestry?Is there any evidence you would accept?

There is no "any nested hierarchy". Either it is a nested hierarchy or it isn't.If common ancestry is true AND vertical inheritance is true, then it should produce a nested hierarchy. That's the prediction. The observation is a nested hierarchy. Prediction supported. Theory supported.When observations match the predictions made by the theory then the theory is supported. That's how science works. Exactly. There is no reason why design would produce a nested hierarchy over any other pattern. Only common ancestry with vertical inheritance will necessarily produce a nested hierarchy.When A predicts billions of possible patterns and B predicts one specific pattern, observation of the specific pattern predicted by B makes B the better explanation. Funny how you can't explain why my reasoning is flawed.

Common ancestry predicts a nested hierarchy. We observe a nested hierarchy. The theory matches reality.

It's called the law of parsimony.

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For, be it observed, the exception in limine to the evidence which we are about to consider, does not question that natural selection may not be able to do all that Mr. Darwin ascribes to it: it merely objects to his interpretation of the facts, because it maintains that these facts might equally well be ascribed to intelligent design. And so undoubtedly they might, if we were all childish enough to rush into a supernatural explanation whenever a natural explanation is found sufficient to account for the facts. Once admit the glaringly illogical principle that we may assume the operation of higher causes where the operation of lower ones is sufficient to explain the observed phenomena, and all our science and all our philosophy are scattered to the winds. For the law of logic which Sir William Hamilton called the law of parsimony—or the law which forbids us to assume the operation of higher causes when lower ones are found sufficient to explain the observed effects—this law constitutes the only logical barrier between science and superstition. For it is manifest that it is always possible to give a hypothetical explanation of any phenomenon whatever, by referring it immediately to the intelligence of some supernatural agent; so that the only difference between the logic of science and the logic of superstition consists in science recognising a validity in the law of parsimony which superstition disregards.
--George Romanes, "Scientific Evidences of Organic Evolution", 1882
The Project Gutenberg eBook of The Scientific Evidences of Organic Evolution, by George J. Romanes, M.A., LL.D., F.R.S.

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Please explain why a designer could not have given bats lighter bones, or birds heavier bones.Please explain why a designer would be forced to fit his designs into a nested hierarchy.

False. I think that a nested hierarchy evidences common ancestry. Hasn't that sunk in yet?If a species had similarities that were derived features from both mammals and birds this would FALSIFY evolution. This would disprove evolution. Similarities can disprove evolution if certain similarities are seen together in the same species.So NO, I am not saying that similarities in and of themselves evidence common ancestry. I am saying that the PATTERN of similarities evidences common ancestry.

Then why are you rejecting the scientific method?In the scientific method, a theory makes a prediction. If that prediction is observed then the theory is supported. You are actively rejecting this logic.

For the same reason that geologic processes haven't produced the Grand Canyon in Nebraska. If there isn't a Grand Canyon in every US state does this mean geologic processes did not form the Grand Canyon?Different lineages take different routes. Evolution proceeds differently in different lineages. Different species go extinct at different times due to changing environments and evolutionary paths. This is Biology 101. What bad logic? Which flawed arguments?

What reality am I ignoring? What sound logic?