Mammalian Middle Ear Evolution

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What I am trying to establish is does ToE actually make any predictions. Or does it just morph the theory to the data?

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I think the term ToE is largely misnomer.There isn't a theory of Evolution instead it is a body of knowledge. What is usually meant by 'the Theory of Evolution' is (the modern synthesis of) what Darwin called Natural Selection. This is a theoretical statement about how Evolutionary change is caused. It makes predictions; but these predictions are not ones that can be tested by the timing of the MME.But alongside Natural Selection you also have the reconstructed history of life on Earth; and this includes a whole body of various theories about when specific changes happened and further theories about what caused the changes. Because these are based on generally weak and constantly updating evidence they change rapidly; and they do make predictions: from the fossils we have already discovered charting the history of the MME we can make predictions about what fossils we'll expect to find in the future and what timeframe we should find them in (and also about genetics and embryology, but that's another story).So, you're right, the ToE does make predictions about when we should find fossils of transitional MMEs; but the others are also right, the ToE doesn't make predictions about these transitionals. It depends on what you mean when you say ToE.Edited by Mr Jack, : Better title

If you'll excuse me quoting myself from elsewhere, I once wrote a longer breakdown of the theory:

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What exactly is Evolution?

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In this discussion, I shall assume we're talking about Biological Evolution or The Theory of Evolution rather than any of the other meanings of the word 'evolution'. I've also chosen to leave out the evidence from this answer, we can discuss that later as you see fit.

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Evolution is the scientific theory developed from Darwin's work Origin of Species - the central theme of which is decent with modification by natural selection. It's a big subject so I'll break it into pieces.

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The first part is Descent with Modification. This simply says that a creatures children are similar but not identical to their parents. In Darwin's time, no mechanism was understood for this process. Modern genetics allows us to understand how it works, and we can now track the transfer and alteration of genes. Genetic copying is not perfect, so each generation contains a small number of errors (which we call mutations).

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The central part of the theory is the mechanism proposed by Darwin: Natural Selection. Natural Selection is really very straight forward, it says that individuals that are more successful will come to dominate the population. In practical terms the success of an organism can be measured by the number of grand-children it has (grand-children rather than children because having lots of children who die young or never breed is no use). It should be obvious that organisms that are having more grand-children will end up forming a larger portion of the population than those who are having fewer. Note that this success (known as fitness) may not correspond to what we would subjectively identify - for example, the fittest bear may not be the biggest and strongest because their energy needs are higher and they could suffer in times of drought.

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This is, of course, complicated by sexual reproduction. In each generation, most organisms do not produce exact copies of themselves but mix their genes in with another's. So what, in fact, we should be looking at is the effect of genes (and the traits they cause) on the success of an organism and what Natural Selection is doing is increasing the proportion of the population that carry the given gene - this is what Dawkins is talking about when he uses the term 'Selfish Gene'.

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When we combine Descent with Modification and Natural Selection we get Evolution. The theory is that over time mutation (and genetic recombination) will produce new solutions to problems (faster running, better wings, better eyesight, etc.) and that Natural Selection will constantly keep picking the one that works best. Now this level of Evolution is not particularly interesting, so far we've got dogs that run slightly faster than their forebears and moths that are a darker shade in industrial cities. The big claim made for evolution is that this mechanism is sufficient to explain the apparent design we see in all life today, including such marvellous examples as an eye, a bird's wing or an ant's social structure. An important point to remember is that evolution is not directed, there is no end goal. At any time it is simply picking what works best. This strictly limits the solutions that evolution is capable of finding since each one must be a step-wise improvement (or at least neutral with respect to fitness).

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And this is were we come to the third portion of Evolution: Common Ancestry. Common Ancestry is the claim that similar organisms today evolved from common ancestors in the past (this is a slightly different claim from the Single Common Ancestor claim I will discuss below), so Coyotes and Wolves evolved from a now extinct Canid, Zebras and Horses from an extinct Equid and humans and chimps from an extinct ape. The evidence for Common Ancestry comes from two main sources: the fossil record and genetic analysis.

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Most evolutionists believe that all life on earth evolved from a Single Common Ancestor, all believe that all animals evolved from a single common ancestors. According to Evolution we can construct trees of ancestry going back into the past, the further we go back the more the species alive today will converge in their ancestry. For instance, all mammals and reptiles converge to a single ancestor around 500 million years ago - the first vertebrate. The direct evidence for Single Common Ancestry lies in the use of DNA throughout all living creatures (viruses, incidentally, are not commonly thought of as alive - although I think they should be - scientists differ on whether viruses and all other life share a common ancestor), the indirect evidence comes from the simple convergence of evolutionary trees which, if extrapolated, leads inevitably to a single point of convergence. If Single Common Ancestry turned out to be false that would not scupper evolution as a whole. This is not true for either of the three points above.

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The final areas of Evolution are Historical Evolution and Non-adaptive Selection. Historical Evolution is the attempt to reconstruct as exactly as possible the actual evolutionary pathways that led from one species to another, and establish the relationships between existing species. Non-adaptive selection deals with genetic change in populations which is not linked to an individuals adaptedness: this includes things such as genetic drift as well as events such as lightning strikes and volcanic explosions.
  —me

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What I'm saying is that when Nosy says the Theory of Evolution does not make predictions about when the MME evolved, he is talking about the Descent With Modification and Natural Selection parts; but what AOK is talking about is the Historical Evolution part. Now the existing historical reconstructions of what exact path evolution took do make predictions about what fossils we will find and when but if these predictions turn out to be wrong all that will be disproved is that part of our understanding of the history of life on earth.Is that any clearer?Edited by Mr Jack, : No reason given.