I would summarize the answer in two words: Nested Homologies.
For the past three years, I studied one particular
type of ion channel (the N-type calcium channel). For those unfamiliar
with that term (like I was four years ago), "ion channels" are specialized
proteins in the cell's membrane that control the flow of ions into
and out of the cell. The ion channel I studied, like most ion channels,
is found in all kinds of species, and tends to have very similar
biophysical properties across mammals, birds, reptiles, even insects.
There are a few regions of the protein which are very sensitive to
mutations, and those sequences tend to be very similar (homologous)
across all species. But most regions of the protein are fairly
insensitive to mutations. You can make lots of amino acid substitutions
and the channel functions pretty much the same. When we compare the
amino acid sequences across difference species, we find that
species which are "closer" to each other (as established by body type
and by the fossil record) have more homologous genes. Species farther
apart have less homologous genes.
This pattern of homology in genes (high homology for closely related
species, low homology for distant species) is repeated in lots of
different proteins. (Remember, in most cases the proteins are
functionally equivalent despite sequence differences.) Moreover, the
pattern of homologies is "nested." For a particular gene, different rodents
have pretty similar sequences to each other, and different primates have
pretty similar sequences to each other, but there are many more
differences when comparing primate sequences to rodent sequences.
However, primate and rodent sequences in general are more similar to
each other than to frog sequences. And frog, rodent, and primate
sequences are more similar to each other than to insect sequences, and
so forth.
So there is a pattern of nested homologies in the sequences of genes.
There is also a pattern of nested homologies in genome organization
(that is, where the genes are located on chromosomes). And there is a
corresponding pattern of nested homologies in the anatomies and the
developmental programs across the species.
And, as a general rule, these nested homologies match the fossil record.
We can't track genes through the fossil record, but we can reconstruct
some of their anatomies through fossils. When we can match modern species
with a sequence of similar fossils going back in time, modern species
with the most genetic homologies to each other also tend to have a more
recent convergence of their fossil lines.
In the above paragraphs, I used qualifying words like "tend to" and
"generally." The picture is still very incomplete. The fossil record
is splotchy in most places. Many (most?) genes haven't even been
identified yet. Most genes that are identified have only been sequenced
in a handful of species. Only a few dozen genes, perhaps, have been
sequenced across a large number of species. But despite the
incompleteness, wherever we look at genes or anatomies or fossils, the
pattern of nested homologies keeps popping up. And when a pattern is
that persistent, it just begs for a comprehensive theory to tie it all
together --- in this case: common ancestry and descent by modification.
Now there are (at least) two versions of "common ancestry and descent by
modification" which fit the patterns of nested homologies:
(1) macroevolution, and (2) a progressive creation in which God
intervenes, at various times during the billions-years history, by
modifying pre-existing forms in steps to make new lifeforms. We cannot
yet empirically distinguish between these two theories.
In stellar evolutionary theory, we *can* empirically distinguish between
interventionist and non-interventionist models. We have enough
knowledge about gravity, electromagnetism, and nuclear forces that we
can construct detailed, empirical models about how stars should form and
develop. We can calculate rates, sizes, lifetimes, and ratios, and
compare those predictions to astrophysical observations. We see that a
non-interventionist model fits the data, so we feel safe in concluding
that it is probably true. But in biological evolution, we can't yet
make detailed empirical predictions like that. Some claim that natural
processes limit evolution to microevolution and that interventions must
be necessary for macro-changes; others claim that natural processes are
sufficient for macroevolution. The arguments on both sides are "hand-
wavy." Hand-wavy arguments are valuable in science, but things don't
really get resolved until we've got the numbers.
So why do our learning institutions almost universally choose
macroevolution over progressive creation? Here's where philosophy
becomes a critical factor.
The three major religious convictions of scientists in our learning
institutions are Judaism, Christianity, and atheism. There are other
religions represented, but right now and even more so in the past, those
three account for the vast majority. For atheists, progressive creation
isn't an option (unless they want to speculate about meddling space
aliens). Progressive creationism *is* a viable option for theists. God
could have intervened miraculously in biological history whenever he
chose; God has intervened miraculously in human history. So why do so
many theists choose macroevolution over progressive biological creation?
The main reason, I believe, is this: macroevolution maintains
consistency with the common theistic perspective in the other natural
sciences --- and particularly the other historical sciences.
We have good empirical models for how stars form and evolve by natural
processes. We have good empirical models for how the earth formed and
developed oceans and an atmosphere by natural processes. We have good
empirical models for how the heavy elements necessary for life formed by
natural processes. The common theistic perspective is that, while God
could have formed these things miraculously, God chose to use the
regular and continual operation of his natural laws in order to
accomplish these acts. Moreover, we believe that God today uses natural
processes (microevolution) under his providential governance to maintain
robust and adaptive ecologies. Thus, to many theists, macroevolutionary
theory seems more consistent with how God formed and sustains all the
other parts of the natural world.
That, I believe, summarizes the main perceptions and perspectives of the
(theistic and atheistic) scientists whom I know personally.
Loren Haarsma