Reaping the Whirlwind: protein function without stable structure


@Raymond_Isbell After 160 years you don’t think evolution has risen to the top? According to a Pew survey 81% of adults believe humans evolved but that doesn’t rise to the “clear to all” level? And then there is the 98% of scientists that agree. By “clear to all” did you really mean “clear to me”?

I would say that “the ID/Creationist sides try to actively suppress their opponents”. I am sure you have called them out for that as you do here. Did you get any response? As far as BioLogos goes did you see this?

I don’t think you can really say we try to suppress other views here. We welcome all that would like to interact here. Unlike other websites that don’t allow comments or suppress the comments from anyone that expresses support for evolution.

(Mervin Bitikofer) #364

This is no minor thing, @Raymond_Isbell! Do this experiment: go to an AIG (or any similar agenda) website and locate an open forum (if they have one) and interact in ways that try to bring truth and accountability in civil and respectful ways. I think you’ll find that if you ask questions that aren’t “on message” with an anti-evolutionary agenda, your comment (and maybe even your account) won’t last long in those settings. Now I could be wrong - I can’t remember the last time I tried this; It’s been a while. But there’s a reason we give up. When open conversation isn’t welcomed, eventually those who don’t align with that message go elsewhere. YECs may feel similar sentiments about Biologos here, but unlike in their own venues, their comments are not just allowed, but welcomed here and even extensively interacted with and responded to.

So which party is it, Raymond, who seem to be most afraid of scrutiny and challenge?

(Dennis Venema) #365

Years ago I tried to sign up for an account at Uncommon Descent, which was (at the time) the leading ID discussion page. I used my real name and an email address that was firstname.lastname@___ . It was refused.

Evolution News & Views published more words about Adam and the Genome last year than I wrote in Adam and the Genome - all on a website that does not allow for comments.

One of the things I really like about BioLogos is that we welcome all comers, whatever their views, and we’re willing to discuss things. We have pro-ID folks here regularly.

(Randy) #366

Yes, this Counterpoints book is a great one, too. It allows Ham and others to have their say (by the way, read the back and Ken Ham insisted on a longer portion than the others–including Old Earth and ID–because he said his was the “only Biblical view”). Given that the others also believe they are following God, I’m not sure how well that went over.

It seems to me that medicine (I’m a family doc) is an apt comparison to science. It’s such a vast field that anyone with knowledge in one area would be primed to ask questions, but would never presume to criticize the other specialty. For example, you don’t want a gastroenterologist or family physician telling an OB gyn how to do a hysterectomy; nor a neurosurgeon instructing an endocrinologist in the secrets of testosterone or the adrenal and pituitary axis.

Thus, an engineer knows a lot about some theories of function–and while that helps with asking questions, about science, would you agree with the parallel illustration of medical specialties, that science has a huge depth that requires more study?.

It’s been said that the difference between a primary care provider and a specialist is that the primary care provider knows less and less about more and more till he knows nothing about everything; and the specialist knows more and more about less and less, till she knows everything about nothing.

However, being a primary care physician certainly provides endless opportunities for reading where I don’t know anything. The Four Views book above is sort of like reading a primary care primer on different views–you would probably find it enjoyable. I did.

You might also want to read John Walton of Wheaton College about the difference between NT and Genesis literality; I really do believe that God’s words are higher than ours; I learn a lot from Pete Enns and his sort of notes.

(Raymond Isbell) #367

Just did a quick review of the Rumraket review of Tour’s Open Letter. Wow. Rumraket lives in fairy tale land. He can’t seem to anchor to any reality. No assumptions allowed or you’re begging the question. That’s a world I’m unacquainted with so I cannot qualify to criticize.

(Randy) #368

yes, I would read all the opinions there; especially @Swamidass.
By the way, thank you for reading there.
thank you for your discussion.

By the way, I can be wrong in many ways, and you are way above me in engineering and systems skills. So please–“mea maxima culpa” sometimes (I am very wrong sometimes).

(Raymond Isbell) #369

It’s human nature to do anything to thwart an idea or action of an opposing party. [political content removed by moderator.]

In this BioLogos discussion, it’s been pretty tame compared to others. I like that since it has allowed me to learn. I’m taking the ID & YEC positions for a reason. In SE lingo it’s call stress testing. I’m trying to stress test evolution as an explanation for the observables.

You guys are a good bunch. A few are grumpy and not as gracious as they could be, but that’s Ok. I have a tough skin. I occasionally have a rough edge, but I’m trying hard to hold it in check. I’ve rewritten several responses to tone it down.

Let’s talk about substance, e.g., evidence. The evolution video I referenced earlier today was a good example of using evidence that is clearly less than confirming even in large numbers. I think you guys can do better. I just haven’t seen it yet. However, if you can’t do better, what does that say about the strength of evolution as a better explanation than ID or YEC?

Since neither of us have a full (and convincing to all) set of evidence, how do we assess the reasoning process of what’s we do have in the way of evidence?

As I think about it, I see three strong points for ID:

Strong points for ID:

  1. The stochastic models imply design,
  2. A systems engineering (SE) perspective suggests design,
  3. Easily inferred from the God given ability for all men to identify things that are designed vs. things that occur naturally.

Strong points for evolution:

  1. Lots of evidence (caveat: evidence is questionable and less than confirming, and open to the eisegesis and extrapolation charge),
  2. Majority of scientists embrace it,
  3. Most popular (?)

Negative points for ID:

  1. Relatively new (1970)
  2. Few adherents
  3. Disguise for religion.

Negative points for Evolution:

  1. No good answer for the mathematical improbability problem,
  2. Evidence is weak and questionably scientific
  3. Gives support to Atheists

Suggestion: Let’s flesh this out a bit. The list above is a quick first pass. Feel free to add points. Don’t remove any unless we both agree. If a point has too many negatives, we can drop it as long as its negative to both sides.

This little drill may be enlightening as it’s unpacked.

(Raymond Isbell) #370

But you’re not grumpy!

(Mervin Bitikofer) #371

Others will want to address many of your other points, but I’ll comment on this last one at least. First of all note that even if this last conjecture was true, it would not be relevant to assessing the evidence on evolution. (Just as the ‘disguise for religion’ also has no bearing on the truth of I.D. though it may have plenty of implications for how its proponents are seen). But that aside for the moment …

I think we could fairly dispute even the truth of the premise in the first place. I would say rather that evolution has been an affliction for a certain mindset towards biblical interpretation. Far from being anathema to Christians generally, it is rather seen as bad for those whose specific understandings of Genesis preclude it. And only after that, and after Christianity is presumed to identify predominately with that specific fundamentalistic set - only then could it be seen as a boon to atheism. Apart from this reactionary mentality, scientific evolution cannot be seen as even being [shown to be] relevant to classical theism or lack thereof.

(Dennis Venema) #372

Raymond, just a note that in case you missed it: I asked you a specific question back up in post 355.




49 years old is “new”? That is 1/3 of the time that evolution has been around.

How about, after nearly 50 years is still not widely accepted.

ID never addresses, AFAIK, the tools used to build the design.

(Raymond Isbell) #374

Sorry that I didn’t get to this. I was cut off from posting more than 3 responses at once. I think yours was next. I then quit for a while and forgot it when I came back.

I’m tired right now, so I’ll get to it tomorrow.

(Raymond Isbell) #375

Again, sorry for the delay in answering this post.

The quote above is odd. You must not be keeping up with the ID literature. The Discovery Institute Center for Science & Culture now has an Engineering Working Group. At a Discovery Institute meeting in Oct 2016 in Calgary, I was discussing some of these concepts with a small group including Stephen Meyer, and he came to me afterwards wanting to talk. We only discussed it briefly but he was intrigued as were others and it led to the formation of their new Engineering Working Group. That’s when I realized I had to start learning biology. I’m making progress, but still have a long ways to go. The Working Group pointed its participants to a paper from Cell Systems titled “What Have the Principles of Engineering Taught Us about Biological Systems?” Here’s a link to that paper: So back to your question, “Why are pro-ID folks who know biology not making the arguments I’m making?” Answer: They are just beginning to see its value, and are starting to dig in.

Wow! I thought I had, at least the more substantive evidence. What comes to mind first is my challenge that the evidence for evolution strikes me as being marginally qualified to even be called evidence. It’s more an extrapolation of hypotheses to cover the numerous data gaps. It qualifies as hypotheses, but not much more. When you recommend as a test “Look at the Fossils.” I have to comment that one must first establish that the incomplete and discontinuous fossil record even qualifies as an arbiter for the test outcome. Surely you see the weakness in such an assumption!

The whale narrative is weak for the same reason. An expectation that the fossils will eventually be discovered to fill in the gaps where you have conjectured their existence is not a valid test criteria. I’m seriously waiting for you guys to provide some real evidence, not the kind that is unproven in a scientific sense.

I am currently listening to an old debate ( which has some good but also bad points. The best was when David Berlinski asked the question to Eugenie Scott, “Can you give us your best estimate of the number of changes required to take a dog like mammal to a sea going whale?” She could not, so Berlinski asked her, “How on earth can you commend the mechanism if you are unsure it’s adequate to deliver the result?” He sees the same weaknesses that I do, and like him, I’m not getting good answers about the mechanism that warrant embracing evolution as the answer. James Tour sees this also as a key question, “What’s the mechanism?”

Regarding your question on primate genes and the claim that they are understood sufficiently to conclude that evolution is true, I have to push back. How so do you understand it? You’ve seen some simple mutation/outcome scenarios, but does that fully characterize the relationship between the genes and their associated functions in an ape and a man sufficient to conclude that there’s no difference? Are your tests really that comprehensive? And if there are, how does that rule out design? Please don’t invoke the rule that says “God wouldn’t do it that way.”

I’m sure I could find plenty of support for it, but does that settle it, especially since the published literature won’t publish views that challenge evolution?

It’s interesting that I see design where you see evolution. The nice thing about the SE world is that you don’t have to rely on people to assess results, you rely instead on test results that rigorously define the test, and the principals and rules of science to interpret them. I highly recommend it. It’s value is asserted in the link I provided above.

You really need to approach confirmation of evolution by more scientific methods, methods that don’t fall prey to biased interpretation.

By the way, Ken Miller in one of the debate segments provided a “clear example of macro evolution.” It was a species of butterfly in Hawaii. It had some new structures in its mouth that enabled it to eat a certain kind of fruit. Reminded me of Darwin’s finches. Not a good example. But isn’t it interesting that evolutionists consistently offer examples of micro-evolution to prove macro-evolution. This will be helpful as we zero in on how to evaluated evidence. Criterion for assessing evidence is going to be the key that determines whether evolution or design best explains the observables.


Perhaps because no one has offered any evidence of a mechanism that prevents small changes from accumulating into large changes. In your ID/Creationist reading have you found anything that would convince me that there is some kind of barrier that prevents this? After all a journey of a thousand miles is taken one small step at a time.

(Raymond Isbell) #377

You mean like something that would prevent a 747 from being formed after a tornado blows thru a junkyard? I can’t think of anything off hand.

(Mervin Bitikofer) #378

Evolution (as scientifically described) is not remotely analogous to a tornado assembling anything in a junk yard. Nobody has ever claimed evolution works or ought to work like that except anti-evolutionists who need a straw man to knock down.

(James McKay) #379

Raymond, if you want to debunk evolution, you need to debunk what real biologists teach about it, and not a completely nonsensical cartoon caricature of it.

You know as well as anyone else does that that is not how evolution is supposed to work.

I’m sorry, but knocking down straw men is simply intellectually dishonest.

(Jay Johnson) #380

Now, a long time ago (#249) you said you weren’t a partisan, but just wanted to learn about evolution in order to make a reasoned (presumably, “objective”) judgment about it.

In case you missed it, @sfmatheson is the editor of a sister publication to Cell Systems, namely Cell Reports. Both are published by Cell Press. Stephen has suggested several avenues of exploration for your stated interests – all of them assuredly far ahead of where the DI “working group” has gone. (I’m not going to go back and look for them. If you’re interested in actually learning rather than debating, re-read his posts.)

In a nutshell, while you could have been asking questions and learning something, you plowed straight ahead with your agenda. Sorry to mix my metaphors, but you really are missing the boat here. Do you want to learn, or just tell us what you’ve already decided?


Even Tour admits the immunity system evolved so that tornado creates a Chevy at least. So micro-evolution is real. The lack of any reason why these acknowledged as real small steps don’t add up to big steps is a major failing in ID. Since you have contacts in DI why don’t you ask them for their thoughts and let us know.

(Chris Falter) #382

If we applied your logic to other scientific disciplines that deal with natural history, much of modern science would collapse.

You (and Berlinski) have been insisting, for example, that all of the details be elucidated for a long 66 million year transition from an ancient mammal population to modern cetacea. If that cannot be fully identified, then the evolutionary transition is really just eisegesis and circular reasoning according to Berlinski and Isbell.

Suppose I, Chris Falter, were to go to astrophysicists with similar demands:

  • Where exactly were the ancestral first generation galaxies and gas clouds that gave rise to the Andromeda galaxy?
  • How many of clumps/galaxies were there and how big were they?
  • How many smaller galaxies were absorbed into M33? How big were they at the time of absorption and exactly when did these mergers take place?
  • You think dark matter and dark energy explain galactic formation? Completely unscientific! You have no idea what they are. How can you include them in your theory? Any theory that includes dark matter and dark energy inherently has huge explanatory gaps from the perspective of mechanisms.

And hey, you astrophysicists, if you can’t answer these questions, how do you expect anyone to believe your theory of galactic formation?

Geology would have similar problems. Solar system evolution. The list goes on.

But maybe you’re right, Raymond, and we should just say God designed everything and call B.S. on the theories in these scientific disciplines, including biology.