The reference that Darren G makes to Dennis Venema's Evolution Basics article is great! It illustrates the main point at a general level. Also the talk by April Maskiewicz Cordero at the BioLogos conference this past April provides a nice oral summary of the basics. However, I would like to add a bit from the context of our discussions with Fuz Rana at Reasons to Believe. Fuz believes that the mutations that seem to be faithfully passed on through the lineage and seem to be such strong evidence for common descent have been placed there by God for functional reasons. In other words, humans, for example, may have what appears to be a specific "genetic scar" because that change is functionally important. Furthermore, if two species share the exact same "genetic scar," it's because it is functionally important to both species. Their presence, Fuz would say is a reflection of design, not common descent from a single ancestor that gave rise to both species. It's a bit of a stretch, because he has no idea why every single one of the hundreds of thousands would be functionally important. But still, he is correct that what we think is a debilitating change, has on occasion been shown to have some new function. He's right it happens sometimes.
The problem with Fuz's argument, however, is twofold. First we know of hundreds of thousands of events of this sort, and even though some of them will take on some new function, it is extremely ad hoc to think of each of those hundreds of thousands of changes having some new yet-to-be-discovered function. In a sense, Fuz is proposing a whole new realm for molecular biology. There is nothing in the science to support the notion that each of the million plus is now carrying out some new important function, but there is much to indicate that this would be an almost unimaginable surprise.
But what is really, really important--and the point I tried to make in the chapter from which the above excerpt is taken is the following. For Fuz to be right, not only would each of the "scars" need to be functionally significant, but the exact beginning and endpoint and constitution of each scar would have to be functionally significant too. For that to be true, we really would need a brand new science of molecular biology. Molecular biology would have to be wrong at the very core of the discipline.
We have talked about this over the years. In essence, as I see it, for RTB, it boils down to the notion that some day they will understand why science seems to be in error, but for now, they will take the Bible, as they understand it at its word and they'll work hard at trying to find out how it is that mainstream science seems to be so badly mistaken.
I am comfortable with that as long as there is no unconscious distortion of the scientific literature (on either side) to try to make it fit one's own interpretation. We have tried hard to have the conversations that would help us through this, the most difficult part of all. There is a subjective side to science, and it is brushing up against that subjective side that has made all of this so challenging at times. My first meeting with the group was in May 2009, just days after the public launch of BioLogos. Francis Collins was on a speaker phone, and I had driven up from San Diego to L.A. to meet in their conference room so one of us from BioLogos could be there in person. It was the beginning of many wonderful times together--always we were treated royally by the RTB group. We differ profoundly and sometimes it was very difficult, but what a joy it almost always was to be together.
By the way, the most wonderful thorough discussion of the "genetic scars" I refer to is in this book by Graeme Finlay. It is a tough read for a general reader, but wow, it comes as close to providing a proof for God having created through the evolutionary process as I have ever seen.