[BroJoeK]

from the article: "These glaring contradictions in the fossil record ultimately provided the basis for the subsequent theory of punctuated equilibrium..."

OK, I'll bite.

There are no "glaring contradictions" in the fossil record, none, zero.
That's because a real "glaring contradiction" would be elephants older than dinosaurs, or humans riding on pterodactyls, and nothing like that has been found.

So what these guys are talking about are alleged "missing links", or "gaps" in the fossil record, gaps so serious some evolution scientists proposed a theory of "punctuated equilibrium" to account for them.
Theory says that species can remain unchanged for millions of years, until something new -- i.e., climate change -- forces them to quickly adapt & evolve or go extinct.

But there are at least two false premises in this idea:

1. "Gaps" in the fossil record claimed to represent absence of speciation, when really, gaps represent nothing more than the rarity of any fossils, which only happen under very unusual conditions.
   We can see this when we consider that the total number of fossil species found so far is just a few thousand, or about one-one hundredth of one percent (.01%) of the tens of millions of vertebrate species which ever lived.
   So gaps don't represent "equilibrium", they only reflect the rarity of fossils.

2. The fact that some fossils from different time-periods look similar does not mean those species are the same, or even closely related.
   DNA analysis shows that every species is changing every generation, and only natural selection holds unhelpful mutations in check.
   But regardless of natural selection, mutations continue and accumulate generation by generation such that after tens or hundreds of thousands, speciation has happened, regardless of how similar the fossils may seem.

   An example might be Zebras, which to most people all look the same, but in fact are divided among different species which don't normally interbreed.

Of course the idea that species can change rapidly is glaringly obvious when we consider man-made species such as domesticated dogs.
They were once wolves, now dogs and all within a few thousand years.
So under the right circumstances evolution can happen very quickly indeed.

But even where fossils suggest similarities and relationships, DNA tells us that, for example, wolves of five million years ago were not the same, and could most likely not interbreed with wolves of today, much less with modern dogs.

from the article: "...some biologists have expressed doubt that the Synthetic Theory... based principally on mutation, genetic variation, and natural selection, adequately accounts for macroevolution, or evolution above the species level."

First, the false premise: that a mother of any species can ever give birth to a child of another species.
Physically, so far as we know, and certainly amongst vertebrates, that's impossible.
But what certainly does happen are small changes in every generation such that over geological time periods different populations of the same species can become so genetically different they no longer interbreed.
Then we call them separate species.

Second, that other factors may also operate in evolution should surprise nobody, but defining exactly what those factors are, and how they work, remains the subject of investigations, experiments and hypotheses.
They represent no more a "crisis in evolution" than would, for example, discovery of a new dwarf-planet in the Kuiper Belt create a "crisis in astronomy".
We already suspect something's there, just not exactly sure what.

[JimSEA]

“Modern evolutionary theory has never been without its problems and controversies—even among secular scientists.”

Name for me one scientific discipline or theory that was birthed full blown without unanswered questions, incomplete understandings, false paths, etc. if your going to say, “Your science is false because it doesn’t answer this or that or another thing.” Now, of course, that is just the argument of the creationists. Kent Hovind has a certain questionable fame for supposed conversations with “professors” where they can’t answer his questions so they are incredibly stupid because the high school science teacher can.

Each scientific answer begets a bushel load of unanswered questions. That’s the way knowledge is expanded.