Reaping the Whirlwind: protein function without stable structure

(Raymond Isbell) #503

For someone who’s already made up their mind, you’re right. Do you trust a researcher who’s covered a lot of ground and has been thorough or one who has only looked at his favorite sources?

(Chris Falter) #504

Are you implicitly asserting that Augustine did not cover a lot of ground and only looked at his favorite sources?

(Raymond Isbell) #505

For those waiting for my next zinger, I’m pausing to read. So much is available! I’m also going back over previous posts and points I’ve tried to make along with responses to see if they’ve been adequately addressed or just dismissed. I’m also thinking about a new thread on the nature of evidence, both legitimate and illegitimate ways to use interpret/use/abuse it, e.g., when is extrapolation a good thing vs when it’s used to cover up ignorance and disguise itself to promote ideas that lack genuine support from any body of evidence. Common descent seems to be a nice story that when overlayed on an extrapolated and carefully selected (cherry picked?) body of facts looks compelling. Will a closer look expose it to be a house of cards? I have procured Dennis’ book “Adam and the Genome” and will read it along side John Sanford’s “Genetic Entropy” to see what comes to surface, fraud or truth? I will also be looking at the radiometric dating issue. Is it sufficiently reliable to support OEC arguments, or is it another example of fraud where selected evidence is used and counter evidence is ignored to build and perpetuate a false narrative? If you haven’t read “Contested Bones,” you owe it to yourself to take a fair look at both sides.

As an aside, I stumbled on to a link by Scot McKnight where he spoke on the “Getting the Gospel Right.” ( I think I could mount a significant challenge his views on soteriology. Is there a place in a Biologos forum to discuss theology?

The variety of candy in this store is delightful. Can’t wait to taste it all!

(Phil) #506

Raymond, I look forward to hearing from you. Regarding theology, we have a lot of theology threads so long as it doesn’t get too far off track. One thing I think you will find here is that it is healthy to challenge ideas, and good ideas can be defended, so long as done with respect and grace.

(Christy Hemphill) #507

Anytime you start a thread, you get to choose a subcategory. Theology/Philosophy is one. Biblical Interpretation is another.

(Christy Hemphill) split this topic #508

2 posts were split to a new topic: Scot McKnight’s soteriology

(Raymond Isbell) #509

I’m finally getting back to this issue that you’ve broached. I’m also reading your book, “Adam and the Genome” and seeing some interesting patterns especially with regard to how you define, view, and weigh evidence. (After some more detailed reading, I’m hoping to open another thread where we can really get detailed on what evidence is, how it’s obtained, ways it can be abused and used improperly, etc.) The most glaring problem with the way you use this “evidence” of slight gene sequence variation in multiple phenotypes is that it is steeped in circular reasoning. I see you use the phrase “strongly supports” often as you look at the data and see only one explanation. You see the same tenuous set of data-paradigm links often enough, and consequently, you believe it supports the paradigm of evolution that you’ve used to interpret the data. Looks like a Merry-Go-Round where only certain riders are allowed on to ride.

What’s missing from a “good science” standpoint is that when you form the hypothesis that all hominids are linked to a common ancestor you are not being thorough in identifying alternative explanations. Good science says you should formulate a strategy for identifying and evaluating the alternatives, and then identify suitable metrics by which the alternatives can be evaluated. Or maybe you’ve done that? If so, please point me to it.

I don’t see this (good science) in your book. You’re essentially using evolution as the metric. You ask the question “Is it consistent with the hypothesis?” I notice that you also use as a metric “Parsimony” or a “parsimonious explanation” where you claim that these sequences come from a common ancestral population and have been slightly modified along the way. You then read the evolutionary paradigm back over data and conclude that it supports evolution, and you call it EVIDENCE! It’s noteworthy that evolutionist using this style of incomplete scientific analysis and call the result evidence. How is this not begging the question, i.e., assuming that evolution is the answer, and then using that as criteria to evaluate the hypothesis?

How many other paradigms are there that may have explanatory merit? How is “design” ruled out? Because it smacks of religion or magic or just that we simply don’t understand the cell well enough to answer? With a foundation that manufactures its evidence with such tenuous reasoning, and obvious limitations (don’t allow contrary data into the discussion), how is that, as a theory, different from a classic house of cards.

Maybe we should not be so quick to rule out things we don’t understand like magic, religion,etc. I’m sure the early American Indians described as magic what they saw when one of their own drop dead with a big hole in their chest after a Pilgrim pointed a big stick at them and it made a loud explosion. Would design have been a good alternative explanation for the phenomenon to magic for the Indian?

I need to get back to reading. But so far, I’m seeing a lot of weakness in what you call evidence and the way you find support for it in the gene sequences. It doesn’t sound very scientific to me, but then, I still have more to read.

I’m musing about our soteriology discussion recently and am seeing a parallel. In the discussion on the meaning of the word “faith” you committed the lexical fallacy called “illegitimate totality transfer” where you conflated all the meanings of “faith” from it full semantic range, and read that back into your soteriology concluding that we are essentially saved by allegiance, and not simple intellectual assent to the truth of the gospel, a historic fact. Are you not doing the same with evolution? You find an observation that “is consistent” with evolution and then take that consistency to establish it as evidence. To me that’s not good science, and it certainly not good theology.

What say you?

(Stephen Matheson) #510

I thought the question was how/whether you had an explanation for the genomic evidence. Is this the explanation you favor?

(Raymond Isbell) #511


(Randy) #512

I would definitely finish the book before describing generalizations. I have read it, and it is complex enough that I think you will get more out of it. No book is going to be perfect, but this is a deep subject. Happy reading and i look forward to your thoughts. Thanks.

(Stephen Matheson) #513

Well first, that’s not an answer. “Design” doesn’t even conflict with “evolution.” But second, @DennisVenema asked a pretty specific question about inactivating mutations in structural genes, and their position in particular genomes. So, either “design” is just a one-word summary of “I don’t know but I think god wants it that way,” which is a non-answer in a scientific discussion, or it’s an actual claim about an explanation. Do you have an explanation for the genomic data? Common descent and multiple facets of evolutionary theory, plus knowledge of physiology in almost every case (GULO, olfactory receptors) provides clear explanation. How does the “design” explanation go?

(Raymond Isbell) #514

I"m working on it. Still reading. As I travel the road, I’m making short stops to make observations. The common ones, however, are as I’ve noted, weak evidence and a failure to be thorough in a scientific sense. Oh, ,I forgot the circular reasoning. Whatever explanation I arrive at it must at a minimum not contain these same weaknesses.

By the way, did you look at the new Scientific American ebook titled, “The Science Behind Debates?” I see you in it (and me, in fact all of us).

(Randy) #515

Drive safely. Audible is neat, if you are using that. :slight_smile:

(Raymond Isbell) #516

Not a literal road, but rather the bumpy road that takes me to all the evidence (or lack of it) for evolution. But thanks for the well wishes.

(Randy) #517

Good metaphor!

(Dennis Venema) #518

You’ve misunderstood me with regards to pistis. I’m not saying that it is always best translated as “allegiance”. It has a semantic range (or maybe the better term is content, as per @Christy above). If you watch the sermon where I preach on this you’ll see what I mean. Sometimes it IS best translated as faithfulness, loyalty, or allegiance. We see examples from the literature of the period where this is the case.

Your claim seems to be that it should never be thought of as faithfulness, loyalty, or allegiance. If so, then Paul has made a very strange choice. He’s chosen a word that has that meaning as part of its range, but you’re claiming that he is specifically denying part of that range. Really? When there are other words in greek he could have chosen instead? Not buying that argument.

As for evolution, your approach to science is not the mainstream one. The one I underscore in the book is the mainstream approach - propose a hypothesis, use that hypothesis to make predictions, do tests, and see what results are obtained. The best science can do is to fail to reject a hypothesis. And yes, the sorts of things I discuss are indeed (very good!) evidence for evolution. They are highly consistent with common ancestry.

Even folks like Todd Wood (a young-age creationist) agree that the evidence for evolution is very strong.

The specific example I’ve laid out for you as a question is one such line of evidence. Do you have an alternative, better, explanation for this observation, or not? If you trust your approach to science more than my (mainstream) one, then I’m curious to see how your approach to science, which you see as superior, handles this sort of evidence.


And the mechanism that results in design is …?

(Raymond Isbell) #520



God’s or space aliens?

If God, did He create and kill off each species as necessary? Is He still creating the new species that continue to show up? What is your evidence for this?

(Raymond Isbell) #522

Are you saying that all the evidence is in and that after careful scrutiny by partisans, they conclude nothing points to God and that we should therefore conclude either God doesn’t exist or he’s not active in his creation? I’d suggest you slow down and go back and examine how you identify and evaluate evidence. That’s what I’m trying to do. I welcome your assistance and contribution.

Think for a moment about “design inference.” When can we legitimately detect design with high confidence? Mt Rushmore? An electric induction motor? A space shuttle? A saturn V rocket? A Boeing 747? A bacterial flagellum motor? An ATP Synthase Enzyme motor? If you find the point where we can move from obvious design to “chance and natural selection,” please let us know. As a scientist, how would you structure a study, and series of tests to get the answer? What criteria would you use to evaluate test results and how would you structure the argument to support identification of the threshold for “design” vs “chance and natural selection?” A series of questions that don’t have answers is probably not going to be allow as answers if we insist on being scientific.

I’m not being sarcastic. These are real and serious questions where we should have good answers before concluding that “chance and natural selection” is the best explanation. Given the fact that we don’t have these answers, how is it that we conclude “chance and natural selection” can produce machines that are much more complicated that machines that we have no trouble in identifying as being designed? Walk me thru the logic that arrives at that conclusion.

Is the fact that we don’t have an answer to your question above, viz., “If God, did He create and kill off each species as necessary?” an example of evidence? How does a question like that (that has no answer) constitute evidence? Is this a new category of evidence? How do we define it and weigh its contribution to our scientific approach to determining if “chance and natural selection” is a better explanation than “design?”

Over to you…