Well from a personal perspective it's hard for me to distinguish, because evolution seems pretty incontrovertible to me.
But I have many creationist friends, and the parts they don't seem to accept as "fact" are:
- Speciation (how given any amount of time we could get things as distinct as flowers and dogs and humans from a common ancestor)
- Emergent complexity (how given any amount of time, small changes in the genetic code could have led to things as complex as eyes and brains and so forth)
- Sentience and self-awareness (how given any amount of time our brains could have evolved to possess this seemingly magical and qualitatively different trait)
Again, I want to emphasize that I don't personally think any of these are great mysteries solvable only by appeals to spirituality. However, I hope everyone reading this could see how there's a bit of a jump from the 'fact' of (say) evolution of drug resistance in bacteria to the 'fact' of longer-term cumulative evolutionary effects like speciation and the eventual emergence of "eyes from non-eyes", etc.
Most of these points rely on the belief that evolution is always made up of slow, small changes in the genetic code. While this is the case most of the time (and enables the fine tuning that we see in many species), evolution can happen very quickly.
Population bottlenecks cause species that were once very fit to no longer be fit for an environment, enabling vastly different organisms to become dominant very quickly.
Then there are phenomena like Chromothripsis[1] (only discovered last year), whereby the genetic code of a cell is literally smashed into thousands of pieces and seemingly randomly reassembled. No one is saying that Chromothripsis is a major driver of evolution, but it is interesting in that massive rearrangements of this nature can still provide cells capable of reproducing. In the case of cancer, where it was first discovered, these cells are even able to reproduce faster than normal cells.
The other thing is that even advanced life like mammals and humans have more than 10 times as many bacterial cells than human cells[2]. Since bacteria can evolve very quickly, they play a very important role in evolution.
The eyes from no eyes makes no sense to me, since the entire array of light sensing capabilities are seen in nature. From eagles to plants. The same is true for many of the examples of emergent complexity that are thrown out there.
>The eyes from no eyes makes no sense to me, since the entire array of light sensing capabilities are seen in nature. //
A few articles addressing eyes from a creationist perspective, the first addresses your point most directly. I'll give author and credentials as it seems fitting.
These, indeed the first alone, should make sense at least of the argument from Christian creationist scientists against Darwinian evolution providing a convincing argument for the undirected formation of the eye.
Interestingly this, http://www.answersingenesis.org/articles/am/v3/n3/seeing-eye, answers a question that I've seen raised about the development of the retina and cornea+lens and how they can possibly combine if they develop separately; it gives a very brief acknowledgement of the retina and rearward parts forming from a brain "bud" and the cornea and lens forming from the over-covering flesh of the to-be-formed eye socket. Of course Haeckel's fraud makes one rightly nervous about assuming 'ontogeny recapitulates phylogeny' but it at least provides an insight in to a potential evolutionary process.
I'm an atheist and believe in evolution but I find these three things hard to grasp as well. I just find it fantastic that seemingly random mutations which grant marginally better chances to survival can lead to all these things.
Those are partially hard to grasp due to lacking knowledge of biology. For example almost all the possible steps between non-eyes and eyes exist in animals currently living today. Simply having a patch of light sensitive skin is better than no eyes at all.
Examples from Michael Behe's book Darwin's Black Box:
Blood's ability to coagulate is a cascading system with over 30 parts. Remove one part and it's fatal for the individual. How could a system like that evolve gradually over time?
He lists quite a few such systems. Bacteria having motors, the cell's operational system, the anti-body system (again a cascading system of large complexity).
The motors are not just motors, they just happen to be motors right now. I think it is the selfish gene that describes the path from a protein structure that facilitates the movement of molecules across the cell's membrane into a motor with a flagellum attached.
These things that are claimed to fall apart when a single step is removed were not there from the ground up to provide that specific function, separately they would have provided different functions and when they fell together in a certain way provided a huge benefit. The little bones in our ears were a part of our skulls before they were requisitioned by the ear.
The issue seems to be that the argument looks at how things are and assumes that it was the only thing that these parts have ever been working towards. That any steps in between were useless until put together in this way. Where it is more accurately a bunch of different things coming together to perform all these different functions.
Don't you think what you're writing as a reply is a bit vague? How would you describe the evolution of the coagulation system? What different systems existed before the coagulation system that fell together into the current system?
From what I remember from the book the coagulation system looked to be one monolithic piece and not built up of smaller systems.
His reply is a bit vague, but as I recall this has actually been studied and it turns out that (for instance) other animals have blood coagulation systems that are lacking several of the 30 supposedly essential parts and still work fine - see e.g. http://creationwiki.org/Blood_clotting_is_irreducibly_comple... and the usual anti-creationism resources. Similarly, the supposedly "irreducably complex" bacterial motors turn out to be made of components that originally evolved for other purposes and were repurposed.
I agree that I was vague, however my response was not intended to be an absolute refutation of every argument that follows that pattern, otherwise I'd be playing whack-a-mole with arguments forever. It was meant to be a general explanation of how the argument makes a large assumption that would be pretty easy to refute with further research. As the person above did with a link.
Also, I did give further reading with the selfish gene for a specific example of a bacteria's flagellum.
The answer is simple -- the fact that one species branches off from another species doesn't mean the initial species must die off. There are any number of counterexamples.
Also, the simian species from which we evolved in fact no longer exists. I emphasize this is just a coincidence and doesn't prove one or another point about evolution.
Darwin's finch species from the Galapagos Islands all coexisted, even though most of them branched off from each other, or from a single initial species. There is no reason to assume a priori that species B, which branches from species A, requires that species A must go extinct.
Honest question: which parts?