Reaping the Whirlwind: protein function without stable structure

Do you honestly expect people to be able to explain the details of entire disciplines, area of study that take people years to master, in a post on a discussion forum? At some point, you have to decide you are going to trust experts. It seems like you are completely unwilling to trust anyone else’s expertise, even when that expertise is validated by all the other experts in the field. If you can’t trust an assessment unless you have personally made it (and you are intent on making these assessments in relative ignorance, because you cannot possibly acquire the requisite knowledge and experience to master every field whose expertise you are doubting in what remains of your lifetime) then this whole exercise you are undertaking is a waste of time. Go golfing.


Your responses to people explaining science to you are very similar to a flat earth guy I interacted with here a few weeks ago. I’m sure it makes you feel more secure in your preferred position to believe that everyone who disagrees with you holds their opposing views because of a lack of character or intellectual curiosity or both. But there is a time and a place for honest, intelligent people to declare an issue settled in their minds.

Not being “open” to alternative explanations to settled issues is not automatically a mental deficiency, it’s part of healthy learning and mental stability. Vaccines are safe. The earth is round. Climate change is real. Evolution is a demonstrable fact. Those are settled issues in my mind, and my unwillingness to open up debate and be “objective” about what “the other side” brings to the table is not a sign of intellectual weakness, it’s a sign that learning has already taken place and I’ve moved on to other open questions.

You are the one who showed up here in a state of ambivalence about what you know and with questions. Projecting your state of investigation on to everyone else and assuming that unless everyone else has the same open questions, they are closed-minded and crippled by cognitive bias is uncalled for.


You seem to have forgotten that I told you I would be playing the devil’s advocate for the sake of debate. Now that we’re getting to essentials and details that matter where the evolution side seems to be wanting, the evolution side is crying foul?

I’m recognizing serious weakness in the evolution side and rather than getting a gracious recognition of those weakness and a way forward that seems hopeful, I’m told to quit and go play golf? Really?

It’s probably just as well. As you may have noticed, there are many scientists who are coming to recognize the same things that I and many other ID folks have learned. Evolution is simply a dog that won’t hunt. Some are slow to recognize it, and because of their deep personal investment in it, they won’t let go, no matter the facts. When finally forced to face their tenuous evidence and weak arguments, they retreat and say, “I believe what I believe, thank you very much.”

I think this well is dry, and it’s time to move on.

I wish all of you well.

It is. It has also been verified in hundreds if not thousands of experiments. These experiments observe which segments of DNA get transcribed into RNA and which RNA segments get transcribed into corresponding proteins. (I might be using the wrong lingo here; biologists, please feel free to correct my terminology.) These experiments have provided the evidence that most of the human genome is non-coding.

Does that make sense to you, Raymond?

I have a junk shelf in my garage where I toss miscellany that I don’t really use, but might someday. So far I haven’t used any of it, but someday I might.

Junk DNA is the same. It is not in use at the moment, but every now and then some segment of it gets pressed into service.

The prediction of evolution is that disabling mutations can accumulate in a segment of DNA whose phenotype becomes unimportant. For example, many mammals though not all have accumulated crippling mutations in the gene that produces vitamin C. It was broken in humans, which is why sailors on long journeys need to eat citrus fruits. It was not broken in horses, who never get scurvy.

Does that make sense?

Some pseudo-genes have no function, such as the pseudo-GULO gene in humans. Others have reduced function or have been exapted into new functions such as gene or cellular process regulation.

Yes. Not only is it possible, but the non-functionality of many pseudo-genes has already been verified experimentally and published in peer-reviewed literature.

Bear in mind that some pseudo-genes have reduced functionality or new regulatory functionality. Real biology is complex. Biologists are not surprised.

I am surprised that you assert this, because you already acknowledged having read the article I posted that links a specific effect (larger spleen, helpful for underwater diving) and specific mutations. I also linked to several articles that link specific effects in cetaceans to mutations in specific genes.

In fact, biologists have established numerous other links between changed functionality (the effects) and specific mutations (the input). One example mentioned recently is the loss of vitamin C generation and mutations in the GULO gene. Other examples include lactase persistence linked to certain mutations in lactase regulatory genes (in humans) and improved apoB functionality linked to a specific set of mutations in polar bears.

So yes, through careful study biologists have established links from effects back to their genetic causes.

You’re asking good questions, Raymond. I hope you find these answers useful.

I do not understand why you are unable or unwilling to respond to this so far, Raymond. Are you planning to give it a go?


There is no such thing as a finished theory in science. Remember all the physics you learned at Stanford? Well, there is not a physicist on the planet who can tell you the first thing about what makes up 95% of the mass-energy in the universe. I am referring to dark matter (27%) and dark energy (68%).

You and I have a couple of choices in our attitudes to the theories of physics:

  1. Declare the whole lot of them appallingly unscientific and based on thinly disguised circular reasoning.
  2. Accept the usefulness of models like relativity and the standard model of particles that are consistent with large numbers of observations, even as physicists acknowledge that they have more work to do.

If you were to voice opinion #1 to physicists, you would not be surprised to hear them vigorously defend the discoveries they have made and the reliability of their theories. You would hear no small amount of criticism of your lack of knowledge about physics.

Or would you be surprised at such a reaction from physicists?

I wonder, because you have been expressing opinion #1 to biologists over and over and over in this forum. And yet you seem surprised that they defend the empirical foundation of their work.

I understand the frustrations of the biologists with you. Dozens if not hundreds of posts ago, I posted links to several different articles that discussed the links between specfic phenotypes (effects) and specific mutations (causes). Nevertheless, just a few posts ago you asserted that biologists have not been able to establish such links.


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My sister and brother-in-law, a retired USMC sergeant major, spent a decade at Parris Island in the '80s. A similar situation there. My niece died of metastatic breast cancer two years ago. Causal connection? No way to be certain … too many variables. However likely it may seem, no one can say with absolute, 100% certainty that her childhood exposure to toxic chemicals was the cause of her cancer.

The scientific medical literature on the causal link between toxic chemicals and cancer would be full of the same phrases. Your exposure to toxic chemicals was consistent with developing bladder cancer. This is how the scientific community in all the biological sciences – not just evolutionary biology – talks about things. They don’t make definitive statements because absolute certainty isn’t possible. So, when you point out the fact that they use language like “suggests,” and when your entire argument basically comes down to that singular fact, you’re not arguing against evolution, but against all of the sciences, including medicine. What if I said toxic chemicals could not have caused your or my niece’s cancer because the doctors and scientists can’t rule out every other possible cause? Would you agree with me? And what if you showed me the scientific literature pointing out the link between cancer and the specific carcinogen found in your drinking water, but I refused to believe it because the authors wrote: “The evidence suggests Carcinogen A causes bladder cancer.”

This is a very weak reed that you’re leaning upon.

Raymond, please think about what you’re saying. Dennis is describing how science actually works, and your retort is “that might be a good approach.” Ya think? Scientists have been using it for hundreds of years now with great success, and no one in any field of endeavor has designed an experiment that met your criteria of identifying and testing all possible scenarios. You realize that human beings are finite, right? We cannot even think of every possible interaction with the environment or with other systems, let alone identify and test them.

In sum, you’re setting the bar for what you count as “evidence” impossibly high. In fact, it’s so high that not a single branch of science would meet your test. You’re playing with loaded dice.

I don’t think you understand what the Intelligent Design movement is trying to accomplish, or what many of us here believe regarding God’s design and involvement with his creation.

ID is not an alternative explanation to evolution. “Designed” is not the opposite of “evolved.” Virtually every Christian here agrees with you that God designed and supervised his creation. The “design” aspect is not disputed. Many people have told that to you, but you still carry on the same way as if you never heard it. So, please listen and let this soak in …

The dispute between Intelligent Design and Evolutionary Creation is not about “design” per se, but about whether such design by an outside, “intelligent” agent can be scientifically demonstrated to have occurred. So far, ID theorists have been unsuccessful, and I personally believe they will never succeed in finding the scientific proof of design that they seek, because such proof would destroy faith, not encourage it. (As you, yourself, mentioned in several posts.)

It’s a fair question. I believe option 1, including the fact that God planned and designed this world. However, I also believe that the Lord’s thoughts are higher than ours, so trying to “reverse engineer” his design according to human thinking and methods of design is a fruitless exercise. With Pascal, I would argue that God has intentionally created our world to be ambiguous. The evidence is and always will be finely balanced, so that humanity, by the exercise of reason alone, can neither prove nor disprove God, but must approach him in faith. Here is how Pascal put it:

If the world existed to instruct man of God, His divinity would shine through every part in it in an indisputable manner; but as it exists only by Jesus Christ, and for Jesus Christ, and to teach men both their corruption and their redemption, all displays the proofs of these two truths. All appearance indicates neither a total exclusion nor a manifest presence of divinity, but the presence of a God who hides Himself. Everything bears this character… He must not see nothing at all, nor must he see sufficient for him to believe he possesses it; but he must see enough to know that he has lost it. For to know of his loss, he must see and not see; and that is exactly the state in which he naturally is.

If the atheist says, “Blue,” do you feel compelled to say, “Red,” even if you also see blue? Denying obvious facts about our world, such as evolution and the age of the earth, isn’t a winning strategy for evangelism. Have you seen the exodus among the younger generation?


Well for me, the reason I see merit is that it seems to agree with the observed facts, i.e. I think evolution is sound science. To me, ignoring what one observes because it does not fit ones worldview is foolish and misguided. Have you considered the option that both God and Evolution can be true? That is why Biologos exists as I understand it.

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Oh… I do like this posting!

I noticed this morning a video posted by James Tour that you guys might find informing. He’s focused on the challenges of abiogenisis, but as I’ve maintained from my Systems Engineering perspective, all of his argument for abiogenesis apply to the reproduction of life once established. Note his comments on the probability of just some parts of the cell.

Hi Raymond,

Hope life is going well for you. Have you managed to stay retired?

I agree with Tour and you that abiogenesis ~3.5 billion years ago has not been fully explained. The OOL research community is working on the idea that the various parts of modern cellular machinery emerged over billions of years. Thus it is not necessarily the case that all of the machinery had to come into existence at once. But there is no OOL theory yet, due to the murkiness of the research landscape, so we’ll have to keep feeling our way through the scientific cave for a while longer.

Once reproductive life exists, the machinery of replication and metabolism is available for innovative exploration, as we have discussed at length previously. I know that you disagree with the consensus opinion of biological science about this, as we have also discussed at length previously. :slight_smile:

Have a great weekend!



Hi Chris,

Likewise, I hope you’re doing well.

Retirement seems more active, probably because I’m doing what I want, e.g., reading up on biology, geology, cosmology, theology, etc. Also, I’ve taken an interest again in economics. From what I see with our debt picture and current monetary policy, the US is in for a devastating recession that may be more challenging than 2008-9. Cheap money has created some scary bubbles, e.g., stock market, housing, automobiles, student loans, and of course, Governments on a global scale. When it pops which could be any time, all hell will break loose. Seems like a perfect storm, the kind I would imagine that sets the stage for the biblical 7 yr Tribulation.

Regarding my quote above, Tour made an insightful point about all the machinery being available at once. He notes from experience as a synthetic organic chemist that if order randomly appears, the very processes that enabled it to appear will quickly destroy it. Note his probability discussion. Also, note (he didn’t say it explicitly) that the well organized ecosystem needed for that first life must also be present, and be sustainable. The same forces that may allow a random initial appearance of that ecosystem will also quickly destroy it. My puny brain looks at this and my jaw drops in awe. Like David said in Psalm 139:6, “Such knowledge is too wonderful for me; It is high, I cannot attain it.”

Without naturally occurring weather the godless world has nothing. God could just poof weather into existence. Why are you going after one natural phenomenon while ignoring all the others that have to be true for atheism to be true?


Hi TJ,
Implicit in your challenge is that evolution (macro, of course) is a natural phenomenon. Has that been shown to be true or is it really the result of some clever narrative based on conjecture, interpolation, and assumptions of evidence that simply don’t exist as illustrated by the Cetacean example. I’m open to your position, but I need to see a better set of evidence. Narrative that unnaturally ties gaps in evidence together sounds good unless you look closely. Most of you are good thinkers with scientific backgrounds so I’m really puzzled that you don’t see the significant problems with evolution that should give you pause. James Tour, Meyer, et al., have given you solid scientific arguments challenging evolution that should at least make you pause and rethink it.

Would you really present the argument above that evolution is a natural phenomenon like weather to Jesus Christ as you stand in judgment as we all will? I suspect he’d graciously suggest you try again and caution you against begging the question (i.e., assuming evolution is a proven natural phenomenon.) If He challenged me at my judgment to defend macro evolution, I’d shudder in fear. The evidence for it is far from conclusive, and given the argument from design, I’d know I was in trouble if I were advocating evolution.

I think if judgment day is going to consist of science exams, then we’d all better be shuddering for fear (and I’m a science teacher saying that!).

[Of course, I can’t think of a better job security scheme than pushing that … “come ye, come ye! and prepare your hearts for eternity with the sacraments only available in my physics and chemistry classes!”]

[English teachers, you’re just out of luck. I think Spanish might be the official language in Heaven by now.]


Yeah. You missed the point. Completely.

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Isn’t all of life science? We speak/hear/communicate, we look, we touch/feel, and we are continually assessing it all, i.e., we reason. We can draw conclusions without all the facts, but that generally results in a bad outcome. You can do it scientifically so that you’re the outcome of the assessment is sound, or you can do less.

When you’re at your judgment, the queries posed to you will be scientifically sound, i.e., the language used will follow rules, facts presented will not be the result of conjecture and interpolation, arguments will follows the laws of logic, and there will be no “begging the question” to support circular reasoning. I doubt that the periodic table will come up or Schrödinger’s cat, but rest assured hunches and feelings will not be allowed as each of us describe our folly. He knows what each of us can be held responsible.

I’ve notice you guys “shoot from the hip.” You’re more interested in being clever and winning an argument than addressing the real issue at hand. I take this stuff seriously, so pardon my failure to catch your point.

I was trying to address one of your points then you went off on a rant (which is every single one of your posts) about something totally unrelated to my post. Then you start talking about whales. You, a person who has never worked on them, tells me, a person who does, is wrong about them because people who know nothing about them says I am. You can’t have a conversation with someone like you. I have also shared papers that address your points and you still haven’t addressed them. We have all addressed your questions and concerns.


I apologize (if this was directed at me.) You are exactly right that I do “shoot from the hip”, and “make light” of serious subjects sometimes when that isn’t called for. Underneath my attempted humor is a very serious point that I am happy discuss. And that is that scientific ways of seeing things, while very admirable and probably even the best approach we have for discerning physically accessible truths, is nonetheless not nearly the end-all-be-all of all truth that you seem to expect it to be. That expectation, I submit, is probably more in line with the way secularists would like you to think than it is defensible from scripture.

I do think we have significant overlap in things that we would agree on … such as all things physical and scientific being included within God’s truth. So if we learn from scriptures one thing and apprehend from creation around us something contradictory, then it is clear that either one or both of our understandings need adjustment - OR - we just realize we’re holding one or more things at a tentative arm’s length awaiting that future resolution if we are ever blessed to reach it.

Actually, you haven’t, and that’s the problem. You introduce non-scientific narrative that belittles your opponent, you declare victory and then drag a caricature around the arena to show your friends. In all of this, you never address the crux of my criticism, viz. your lack of evidence. Instead, you modify the existing narrative (e.g., “cells are robust)” to provide the appearance of a science based rebuttal. As I’ve said before, show me some good science to support your claims. You haven’t because you can’t, and you can’t because there is none. When you hear a good scientist present a case against evolution, you ignore it such as the latest post by Jame Tour. Tour’s argument blows evolution out of the water, yet none of you see it.