1. Haldane's Dilemma (my personal favorite)
Go to Walter Remine's website for an excellent explanation of the issue.
In a nutshell, the human and primate split happened (last common ancestor) about 6.5 million years ago, but let's use 10 million years for the ease of mathematics. The human genome has 3,000,000,000 nucleotides ("pieces of DNA) and let's say chimpanzees do also. Both have a scientifically accepted generation of 20 years (i.e how many years it takes them to reproduce; some flys are 10-12 days). Now we've all heard that there is a 2% difference in between the human and chimp genomes (false, but we'll skip that for now) so that means there needs to be 3 billion x 2% = 60,000,000 changes.
The numbers are approximate, but the main idea is that 10 million years is not enough time for the propagation and domination of those genetic changes.
Note: Keep in mind that when you hear about the 2% difference is not putting human and chimpanzee DNAs side-by-side and that they only have a 2/100 DNA differences. I mean humans have 23 pairs of chromosomes and chimps 24 (doesn't that already eliminate the 2% difference). According to the Chimpanzee Sequencing and Analysis Consortium, there are "35 million single nucleotide changes, 5 million insertion/deletions, and various chromosomal rearrangements." This puts the number at little over 1%, but stating all these changes in the light of Haldane's dilemma should show us how unlikely all these changes could've happened in the last 6.5 million years or so.
2. The Sea Anenome's Genome
How can the Sea Anenome, a creature that predates bilateral symmetry, have the genes for breast cancer?!? How could evolution know to put them there?
Sea Anemone Provides a New View of Animal Evolution. SCIENCE VOL 317 6 JULY 2007
Moreover, the anemone genes look vertebratelike. They often are full of noncodingregions called introns, which are much less common in nematodes and fruit flies than invertebrates. And more than 80% of the anemone introns are in the same places inhumans, suggesting that they probably existed in the common ancestor [750 Million years ago]...Finnerty and his graduate student James Sullivan also looked in the anemone genome for 283 human genes involved in a wide range of diseases... Moreover, in a few cases, such as the breast cancer gene BRCA2, the anemone’s version is more similar to the human’s than to the fruit fly’s or to the nematode’s.
Here's the link to the summary and the full article
3. Deletion of Ultraconserved Regions Produce Functional Mice
How can regions of the genome that have been ultraconserved (ultraconserved elements have been defined as a group of extremely conserved sequences that show 100% identity over 200 bp or greater between the human, mouse, and rat genomes) be so unimportant? If evolution went so out of its way to conserve these areas, why are they so frivolous? Think, if you had some of your heart and brain genes deleted (which are presumably highly selected for) would you live?
Link to the article
4. The Genes for Limbs Already in Fish
How can the instructions for limbs before they are needed be in fish?
Link here at physorg.com
Long before animals with limbs (tetrapods) came onto the scene about 365 million years ago, fish already possessed the genes associated with helping to grow hands and feet (autopods) report University of Chicago researchers in the May 24, 2007, issue of Nature.
5. Genomics and the Irreducible Nature of Eukaryote Cells
That is the original title of the article - I SWEAR!
Basically it smashes the idea of prokaryotic to eukaryotic evolution. Obviously, the authors still believe in evolution, but its nice to see this concept of endosymbiosis seriously reconsidered. Remember from a design standpoint , its easy to see b/c of the design constraints of a prokaryotes that they could not have mutated or "fused" into what we know as eukaryotes. This eliminates (makes highly dubious even from an evolutionary standpoint) one of evolutions prized idea that Creationist have known to be false for a long time.
Here's the Link to the article, hopefully you can find access for it at your school or library.
Extra Credit: A clear point for Design Theorist
There is this whole idea of "Junk DNA" which scientists thought were evolutionary remnants, of you guessed it, worthless/junk DNA, that just stayed in our genome. Prominent evolutionary proponent and professor of Biology at Brown University said :
While, prominent Intelligent Design proponent and professor of Biochemistry at Lehigh University, Dr. Michael Behe predicted in his book Darwin's Black Box that Junk DNA, would have a purpose.
From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants of the past history of the b -globin genes.
Ken Miller, Life's Grand Design Technology Review Feb/March 1994 Volume 97 (2):24-43
Guess who won? You got it - Dr. Behe.
Encyclopedia of DNA: New Findings Challenge Established Views on Human Genome
Much thanks to Uncommon Descent for this one.
Another prediction that Creationists got right and Darwinist got wrong - The Appendix!
Darwinists predicted that the appendix had no function, while the Creationist (from a design standpoint) predicted it did... who won? You got it Creationists.