It is no surprise that there are scientific problems with evolution. Its predictions are continually turning out to be false. It undoubtedly ranks number one in faulty expectations. For instance, one of its primary predictions, common descent, has badly failed. The reconciliation of the molecular and the visible, morphological, features has been a major problem in trying to resolve the evolutionary tree. The molecular and morphological features often indicate "strikingly different" evolutionary trees that cannot be explained as due to different methods being used.
The growing gap between molecular analyses and the fossil record, concluded one researcher, "is astounding." Instead of a single evolutionary tree emerging from the data, there is a wealth of competing evolutionary trees. And often what evolutionists conclude is downright strange. Over time insects must have evolved wings, then lost them in the evolutionary process only then later yet again to evolve them (or less parsimoniously, the wings could have disappeared over and over throughout the tree). Or again, bats must have independently evolved, in separate lineages, the same intricate echolocation capability.
As one researcher put it, "Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves." These are not minor statistical variations and the general failure to converge on a single topology has some researchers calling for a relaxation from "tree-thinking."
And this is but a sampling of the many falsified predictions of evolution. There are many more where these came from as evolutionists are constantly surprised. You can see 14 basic predictions that were falsified here. Predictions which evolutionists are absolutely sure of are routinely found to be false. "I about fell off my chair" is the typical refrain of evolutionists.
Obviously the scientific evidence does not bode well for evolution. One way to evaluate the theory is with Bayes' theorem which states that for any given scientific observation, O, the probability a theory, T, is true, given that observation, is the probability of the theory prior to the observation multiplied by the probability of the observation given that the theory is true, divided by the probability of the observation without knowing whether the theory is true or not. It sounds complicated but the formula is simple:
P(TO) = P(T) * P(OT) / P(O)
Bayes' theorem gives us a way to evaluate a theory given a series of observations. A difficulty, however, is that the probabilities are difficult to gauge. What is P(T), P(OT) and P(O)? What we can do is use a conservative computation, giving evolution favorable treatment at every turn.
Consider the ratio P(OT) / P(O). If an evolutionist is certain that observation, O, will not be observed, then the numerator should be quite low, say one in a million or one in a thousand. If P(O) is 0.5 then the ratio would be 0.000002 or 0.002, respectively. But to be conservative, and give evolution favorable treatment, let's set the ratio to 0.2, orders of magnitude greater than is reflected in the evolutionists expectations.
For our 14 falsified predictions, using these extremely conservative values, Bayes' theorem tells us that evolution is a one-in-a-billion shot. This calculation is conservative, and there are many more falsified predictions for which to account. But you can see the religion behind evolution did not lead to a very good scientific theory.