Dear Ken:
Thanks for a most civil and constructive response. Your post is in marked contrast to the atheist PZ Myers’ venomous response on his blog to my suggestion on Salon that evolution and belief in God were compatible. I would say that the atheists are much more uncomfortable with this discussion than the religious believers!
While we certainly grew up on opposite sides of the planet, our childhood faith experiences were very similar. Perhaps that is a basis for a mutual understanding over the course of this debate. While I disagree with you in places, I certainly understand exactly where you are coming from.
In my own Christian journey, I have become convinced that we must take God’s revelation in nature seriously. In fact, I think that we cannot understand the Bible unless we do. Let me provide some historical examples that illustrate what I mean:

1) Augustine and many other Christians living during the first millennium thought there were no people living south of the equator. The belief was based on the Bible. These “antipodes” (so named because their feet would be pointing in the opposite direction from Europeans), were ruled out on the basis of the following New Testament reference (Romans 10:18): “But I say, Have they not heard? Yes verily, their sound went into all the earth, and their words unto the ends of the world.”
Augustine and his generation inferred, quite reasonably, that these “words” could not have made it to Australia. Certainly nobody from the middle east could have traveled there with the message of the gospel. Therefore, there could be no people in locations that were too remote to have received this message, these “words.” Global exploration forced a new interpretation of this passage, however, as antipodes, like you and your fellow Australians, were discovered all over the world.
Now, you might be tempted to say that this is just hyperbole or exaggeration on the part of the Biblical author, but my point is that many faithful readers of the Bible continued to interpret it in this way until after global explorations proved that this reading was untenable. You can thus see that, whatever the actual content of the biblical message, the received message was wrong, until corrected by secular knowledge. And, unfortunately, we have no way of knowing what the actual content of the biblical message is. All we know is what we think we are reading.

2) Christians at the time of Galileo thought the Bible taught that the earth was stationary. Psalm 93:1 seems very clear on this, and Galileo was forbidden to promote astronomical ideas in conflict with this Biblical teaching. Subsequent developments in astronomy have provided a new interpretation of this verse.
These are just two examples, but it seems to me that secular knowledge, of which science is a prime example, has aided greatly in clarifying the meaning of Scripture. I am happy to see that you have come out strongly against the claim that black skin derives from the “Curse of Ham” (an unfortunate label, in this case, Mr. Ham!), but there were many people in America in the 19th century and even into the 20th who interpreted this biblical story as supportive of racism. But science has helped us greatly in establishing that “races” are just cultural labels, without meaningful biological characteristics. There is no “Curse of Ham.” Nor is there a “Curse of Giberson,” thank God.
Over and over again, we find scientific knowledge clarifying the biblical message in important ways. History makes a compelling case that the Bible is often confusing and even misleading to those who would read it without the benefits of science and other forms of secular knowledge.
The second point I would make in response to your post involves your claim that “origins science” is somehow different than regular or “operations science.” This distinction doesn’t hold up very well under scrutiny, as the following examples indicate:
1) When we observe distant stars, such as those in the Hyades cluster, we are looking at light that has been traveling through space ever since Captain Cook set off for Tahiti. This light contains electromagnetic information about processes on that star that took place centuries ago. In the same way we can look back in time at events in the universe that took place thousands, millions, and even billions of years ago, the light on these long journeys is like a photograph mailed from across the universe. It faithfully records the distant past, just as a photograph of you as a child faithfully records the recent past. Just because this light has been traveling for a long time, does not mean it has to be studied in a different way than light that is being created in our laboratories today.
2) We can count tree rings that take us back in time. To do this, of course, we have to make “assumptions,” but it seems to me these assumptions are so reasonable that we should not even call them assumptions. In the case of tree rings, we can observe rings being produced each spring on trees. Is it a dangerous assumption to suppose that the rings from 10 years ago were produced in the same way? What about the rings from 100 or 1000 years ago?
3) Theories of origins are developed and tested in the same way as theories of operations and, in fact, the same theory often applies in both cases. Consider General Relativity; this theory was developed by Einstein in 1915 to illuminate how gravity works. Shortly after, it was discovered that the theory suggested that the universe was either expanding or contracting. This is an “operations” application. But within a couple of decades, General Relativity had given birth to the Big Bang Theory. This theory predicted the existence of an unusual radiation that was discovered in 1965. This radiation has been measured and observed many times since. So we can see that our best scientific theories include both insights into present and past processes, and there is no clear distinction between the two types of investigation.
You have made the claim that “Logically, the only way one can be sure of coming to the correct conclusion concerning the origin of the universe and life, is to know someone with all knowledge, who can be totally trusted to reveal to us what happened. Only the God of the Bible can do and has done this.”
I see both of these claims as assumptions. In the first place, we have come to the “correct conclusion” about a lot of things without having an omniscient guide to the truth. Who would deny that the earth is round and orbits about the sun? Or that Jupiter has moons? Or that many of our genes are the same as those of primates? But we discovered those things on our own, by diligent study of God’s creation.
Your second claim, that the “God of the Bible” has given us this knowledge, is a questionable assumption. The Bible does not even claim for itself that it contains a scientific picture of the world. Most scholars find ample evidence of ancient cosmologies in the Bible, such as the references to a solid dome in the heavens, holding back the water. Also, if we want to be technical about it, claims that the Bible makes about itself are at best circular arguments.
It seems to me that you reinterpret scripture every time a compelling discovery about the world forces you to do so. If Scripture was intended by God to be read literally, then this would not be necessary–we would be able to anticipate discoveries, not have to adjust our interpretations after the fact, as we had to do with the motion of the earth.
Your handling of the data from pseudo-genes seems strained and is indicative of what I think is a failure to acknowledge both the integrity of science and the legitimacy of God’s revelation in nature. Implicitly I think you are acknowledging that pseudo-genes pose some challenges but you are claiming you have a response to those challenges. But is your response reasonable? Your argument seems to run like this:
1) Pseudogenes, if they are indeed non-functional, provide evidence–not proof–for common ancestry.
2) Some pseudogenes have turned out to be functional and thus cannot be used to make this argument.
3) Therefore all arguments from pseudogenes can be dismissed.
An analogous argument from the Bible might go like this:
1) Biblical admonitions, if they are interpreted by Christians to support things like racism and sexism that go against the message of Christ, provide evidence–not proof–that we should be careful in how we interpret the Bible and to make sure that individual passages are interpreted in light of the whole biblical message, and not in isolation.
2) Some Biblical admonitions are universally helpful and have never had dangerous misinterpretations. You certainly cannot argue that Christ’s command to “Love your neighbor” has been misinterpreted in ways that are negative.
3) Therefore, concerns that we must be careful in interpreting isolated passges in the Bible can be dismissed.
I cannot imagine you would buy the logic of the second example. So why do you reason that way in the first example? In both cases the reasonable approach is to go with the preponderance of the evidence, to travel the most likely road. In neither case is there an absolute guide to truth.
I would like to challenge your assertion that “There is no rational reason to think that in all cases similarity implies common ancestry.” In cases involving paternity suits we do conclude this. I would agree that we do not have absolute certainty on these questions, but then I don’t believe we have absolute certainty anywhere, unless we simply choose something arbitrarily and say it is absolutely certain–like the Bible or science or some guru or astrology or whatever strikes our fancy. Our goal should be to pursue what is most likely. And, when it comes to genetics, there is no controversy among geneticists that there is solid evidence–not proof–for common ancestry.
This whole debate is based on your question, which you have put elegantly and succinctly: “Which worldview (biblical creation or evolution) can account for human experience and reasoning in a way that is consistent, non-arbitrary, and makes sense of Christian doctrines?” But this is not the right way to ask the question. We are not confronted with a choice between two non-overlapping worldviews. We have the Bible, we have our traditions of interpretation, and we have science and our experience. All these things have to be balanced and weighed against each other. Each must be allowed to speak its own message. If we build our astronomy on the Bible, we will be led astray and suppose, like the critics of Galileo, that the earth does not move. If we look to biochemistry to establish eternal life, we will likewise come up dry. This is a complex problem–I discuss it in more detail in Saving Darwin: How to be a Christian and Believe in Evolution.
It would be wonderful if we had a shortcut to absolute truth, but I just don’t think we do.
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