Reaping the Whirlwind: protein function without stable structure


(Dennis Venema) #343

You’ve actually had several direct answers over the course of the thread that do not involve evolution, and you’ve been given suggestions to learn more (because your knowledge is limited, and interfering with your ability to understand the answers).

I’ll try once more to explain things. We’ll see how it goes. The following is a bit simplified, bear in mind.

Proteins do their job by taking on certain shapes and using those shapes to do various functions in the cell. Almost all of the time those functions require proteins to interact with each other in some way.

Proteins are made of of amino acids - a string of them that folds up into a particular shape.

We know from direct experimental tests that proteins can vary quite a bit in their sequence and still work just fine. Changes in their amino acid sequences don’t drastically change the shape or function of the protein in most cases.

This means that as changes are introduced into proteins through mutation in their DNA code, that most of the time it is not detrimental. Sometimes it is, of course - but most of the time it is not.

We know this from direct experimentation.

This property of proteins means that they are rather resilient to mutations (on the whole).

As changes occur to one protein in a system, it alters what changes are acceptable in its binding partners (other proteins).

This is one reason why cells are resilient and robust. There are other reasons as well, and those reasons are also understood (and have been discussed in this thread).

Does this make sense to you? Do you have questions about it?


#344

While you believe their model and therefore the impossible odds that it generates I don’t. I have seen the explanations on why the model is wrong and the research that backs that up. While I don’t have the knowledge to judge the basic research I accept it.

I accept evolution as the best explanation for the common descent that is apparent to anyone who has looked at the fossil record. I accept the cell has been designed by God but not that we will ever find proof for this. Just like I accept the process that generates rain was designed by God but again there is no proof for this. Do you have any problem with accepting the validity of a weather forecast even though it doesn’t mention God?


(Raymond Isbell) #345

Thanks Dennis for “trying again” to explain it to me. However, what you laid out is pretty fundamental and not really new to me. Apparently, you and others have the impression that I don’t understand it. I think I do, and indeed, if forms the foundation of my argument against evolution. This is the strange and interesting part of this discussion. We each think the other doesn’t understand us.

Your short summary following the quote above affirms what most know (me included) about the link between genes, amino acids and proteins, and their folds and functions. Not much mystery in it except for its origin. I also recognize that proteins can vary quite a bit “in their sequence” (Not sure about what you mean by this, viz., do you mean amino acid sequence?) and still work fine (this poses another question, “work fine for what function(s)?)

In the INCOSE papers they refer to linear causal chains as an important element in complex systems. Do biologists know the extent of those chains in protein functional processes and how far they extend? Has it been shown that a variation in a protein might cause a problem well down the chain, but not be perceptible in early segments of that chain? If current research only looks at the early segments of the chain, it will never detect the downstream effects of a mutation. Do biologists even know the extent of those chains and the functions they support? I suspect they do not which makes it even more surprising that you believe the entire functional organization of the proteins could have come about by chance.

If there’s one thing that stands out as I look at the cell, it’s that its complex structure and functional organization are far from being understood by biologists sufficiently to conclude how they came to be. James Tour affirms this emphatically. Are Tour and Isbell just too simple minded to see the merits in evolution? The bold assertions made by you and others that the “evidence” is overwhelming in favor of evolution as the best explanation for the cell is very puzzling. I would be more inclined to believe that the Presidents’ busts at Mt Rushmore are the result of wind, rain, heat, cold, thawing and freezing over millions of years. Which do you think is more likely, Mt Rushmore or the Cell?

In your last post you say, “This property of proteins means that they are rather resilient to mutations (on the whole).” I assume that you base that on extensive experimentation and testing. But experimentation and testing of what: Your limited understanding of the cell? I recall watching my students (I taught EE at the Univ. of Missouri in the 1980’s) formulating tests to verify a circuit function and could see how their lack of understanding of the circuit elements and their individual and combined functions would lead to tests that had limited value and would often lead them to false conclusions. Good test design requires a deep understanding of what you’re testing and the conditions under which the test is performed. Do your tests in biology that identify function in proteins have sufficient scope to account for deep chain effects? Can the test results conclusively link those deep chain effects back to a mutation? And keep in mind as function is working thru the causal chains, there may be inter-dependencies that can generate side effects that propagate down through other causal chains and in the end be detrimental And that detriment may not be immediately detectable. It may only generate an instability that won’t manifest except under very specific conditions (an inference from complexity). (Software engineers know this well.) If you don’t have a complete mapping from gene to protein to function down the primary causal chain, and other side chains to its end, is it wise to say you know fully the extent of a mutation sufficient to conclude it’s not deleterious?

This quote points back to the circular reasoning I’m seeing in the biological literature, that I pointed out to Stephen. It’s hard to believe you actually said that most mutations are not detrimental. (No doubt you say that because you believe that the RFR present in the cell came from evolution before RFR had evolved in. I guess RFR is not needed?) What I see from modern biology is a conclusion that cells are resilient and robust based on tests that are designed by people who only partially understand how the cell works. They have a mixture of good understanding of some parts of the cell with a lot of biased hypotheses with predictions and testing designed to show a hypothesis true whether it’s true or not. What I see is a culture of conformity where science has become a bludgeon to force everyone to believe a narrative that will get a researcher funding, a professor tenure, and general acceptance of scientists among peers. The reasons I’m seeing in this forum for accepting evolution are not compelling. This cultural bias is so strong that evolutionists resort to mocking and ad hominem attacks on anyone who will challenge them. They block attempts to teach students ID or Creationism in public schools based on their labeling them as Religion so they can employ Constitutional barriers. Evolution so far from what I’m seeing from this forum is founded on industrial strength bias, circular reasoning, mockery of critics, and a lack of humility. I’m not seeing any substantive evidence or argument that supports evolution. I keep asking for it, and all I get back is rhetoric about how little I understand about biology. I’m not the smartest guy around or the sharpest knife in the drawer, but I’m well educated in the sciences, broadly educated in history and theology, and I do think critically with minimum bias. If anyone is trying to understand evolution and see its merit as the best explanation for cell structure and function, I’m a good candidate. So in answer to your last question, “Do I questions about it?” The answer is yes.

In my mind, the single strongest argument against evolution is its unlikelihood. Chance and natural selection (when it even applies) seems to me to be a dog that doesn’t hunt. Are there any good rebuttals you know of for the ID models? Those models, if true, are devastating to the theory of evolution. I’ve brought them up numerous times in this discussion, but I haven’t seen a response yet.


(Stephen Matheson) #346

That should have clued you in to something you can’t seem to compute: that you didn’t understand. You will make so much more progress if you ask yourself this simple question: “if a subject matter expert says something that seems obviously wrong to me, could it be that I don’t know enough about the subject?”


(Stephen Matheson) #347

This:

Is followed by this:

Which is followed by an ad hominem diatribe about schools, “Religion,” and, hilariously, “lack of humility.”


(Raymond Isbell) #348

Are you talking about me or you? From my perspective, your lack of knowledge about basic engineering science is why you can’t seem to understand the argument.

Does a SME employ circular reasoning to argue his position?


(James McKay) #349

The problem, Raymond, is that this discussion is not about engineering science. It is about biology.

I’m sorry, but claiming that an expert in biology can be wrong about biology because he doesn’t understand engineering science is simply absurd.

It’s like saying that an expert in seventeenth century Chinese literature could be wrong about seventeenth century Chinese literature because he doesn’t understand quantum mechanics.


(Raymond Isbell) #350

That’s not what I said. I said his circular reasoning makes me wonder about his authority to speak in support of evolution. If evolution is true, why employ logical fallacies to defend it? Besides that, there are many scientists who don’t agree. Go watch this short video by James Tour, and ask yourself if you can explain evolution to him. He has a standing offer to anyone who can explain it. No one has responded. Listen carefully and ask yourself how confident you are in evolution.

You guys are trying to convince me that evolution is correct. I’m open to being persuaded. However, the attempts so far are sending me back to ID and Creationism as better explanations. Why is that? The claim is that I don’t know biology. But I do know engineering, and the narrative so far for evolution is violating some basic engineering science.


(Chris Falter) #351

More or less. Maybe a better analogy is claiming that meteorologists are wrong about the origins of tropical storms because they don’t understand quantum mechanics. For, you see, quantum effects are part of physics, and physics undergird meteorology.

Hi Raymond,

You are going to need a classical education in biology to understand it. Just reading articles (especially the abstracts by themselves) without the background would be like reading a software system’s dependency tree without any background in computer science. You simply are not going to understand the subject by reading a few details. You are lost in the forest, and want to find your way out by examining the bark of the nearest trees. Ain’t gonna happen.

Here is a list of good books on the subject. You seem to have plenty of time and resources. Why not read one or two books a month (especially from the top of the list) and come back to us after you’ve read a few? We will then have a common understanding of the subject that will help us to have productive discussions.

As it is, the discussions have been 100% unproductive for a long time. You should recognize unproductive meetings when you see them! :wink: I’m sure you’ve been in more than a few.

Yours,
Chris


(Raymond Isbell) #352

Perhaps to you. I’ve learned a lot and it’s been enlightening…but not the way you think. It has confirmed much of what the Bible says about mankind.


(James McKay) #353

It may not have been your intention, Raymond, but it’s what I understood you to be saying.

Maybe I may have misunderstood you there, but if other people had the same misunderstanding (and only they will be able to confirm or deny it) then you may need to consider whether or not you are communicating clearly.

In any case, my point still stands: you cannot just take principles from one area of study and apply them without qualification to a completely different area of study. If you wish to use principles from engineering science to argue against evolution, you need to provide a solid justification as to why those principles should also be considered to apply to cell biology and biochemistry. In the absence of such a justification, you are merely making unsubstantiated assertions.

Could you provide me with a short summary of what was circular about his reasoning? (Bear in mind that I explained what does and does not comprise circular reasoning in a previous post on this thread.)


(Raymond Isbell) #354

I’ve pointed it out at least twice with a specific example. See my post #337.


(Raymond Isbell) #355

I would strongly recommend you watch the James Tour video that I linked.


(James McKay) #356

Thanks Raymond. Wading through over three hundred lengthy posts to find what you are talking about is a thankless task, so some pointers are always welcome.

However, I did point out in the post to which I linked that reasoning is only circular if there are no other lines of evidence involved. As @Randy pointed out in post 338, this is simply not the case:

When you have multiple lines of interconnecting evidence, you can construct at least some of it (in fact, typically most of it) into a directed acyclic graph. And when you do that, you are no longer dealing with circular reasoning, but inductive reasoning and cross-checks. And that is a different ball game altogether.


(Dennis Venema) #357

A few comments, more or less at random:

I’m a professor at a Christian liberal arts university - I’m under no pressure at all to conform to evolution. If anything, accepting evolution, as I did back in the mid 2000s, was seem as a threat to me gaining tenure, not the other way around. I’ve also had pressure to abandon my interest in evolution from various quarters along the way (as well as support, so it goes both ways, just so that’s clear).

I mentioned before that pro-ID folks who understand biology don’t make the arguments you’re making. That should be a sign to you that even though they share your convictions, they realize that your arguments are untenable. If you doubt this, I would encourage you to propose your ideas to some supporters of ID such as Behe or Axe, and let us know what the results of those conversations are.

You haven’t interacted at all with most of the evidence that has been presented to you. As a refresher:

Let’s highlight this one, since it’s a good example of comparative genomics evidence, and you’ve as of yet (as far as I know) not interacted significantly with any genomics data:

First off, feel free to ask questions if anything in that quote is unclear. If you are satisfied you understand it, would you care to offer an explanation for this phenomenon? We observe it over and over and over again.


(Chris Falter) #358

Some questions for you, Raymond:

  1. Are you referring to man’s folly?
  2. If so, do you think it applies equally as well to you as to anyone else?
  3. Are you saying that you are not interested in reading the popular literature written by evolutionary biologists that I recommended to you?

Blessings,
Chris


(Chris Falter) #359

Hi Raymond,

When you stop at the abstracts of the reading material suggested to you, and when you keep repeating the same arguments without taking into account the evidence offered to you in the discussion (such as genomic evidence, reinforcement learning, evolutionary algorithms, etc.), the natural tendency is to assume that your knowledge of the subject is not very deep.

It would take you hundreds of hours to read all the literature/articles recommended to you. Based on your background and on the fact that you have written several book chapters in this forum, I am inclined to believe you enjoy challenges, you have passion about this subject, and you have more spare time than you used to. Why not embark on the voyage and read deeply?

I have actually suggested several to you that you have never responded to in the least.Likewise for many of the arguments made by other friends in this thread. Thus I am puzzled as to why you are asking this question. Your question has already been answered, but the answers seem to have eluded your notice.

I have looked through Tour’s publication list and I see that he has written exactly one piece on origins:

Tour, J. M. “Are Present Proposals on Chemical Evolutionary Mechanisms Accurately pointing Toward First Life,” In Theistic Evolution, A Scientific Philosophical and Theological Critique, Moreland, J. P. Meyer, S. C.; Shaw, C.; Gauger, A. K.; Grudem, W. Eds. Crossway, Wheaton, IL, 2017, pp 165-191.

This one publication of Tour’s is not even about evolution, because the theory of evolution assumes the first reproducing cell(s) and explains what happens after that. It is similar to the Big Bang theory in astrophysics, which simply assumes the initial singularity and explains what happens after the first 10e-39 second has elapsed.

We don’t say the Big Bang theory is circular and biased just because it makes an assumption about a starting condition. We just say that it is not a theory about everything; it has a defined scope. The same applies to the theory of evolution. Biologists cannot explain how the first cell came into being: So what? The theory of evolution is unaffected.

Really smart software engineers have closed bugs on the basis of inability to reproduce the behavior. This means that they were unable to link deep chain effects back to a mutation in code.

But just because they don’t know everything doesn’t mean they don’t know anything. They are able to link some effects back to mutations in code.

The same is true for biologists. Is there some reason to expect them to be omniscient?

I have made plenty of code mutations that I only understood partially. They have nevertheless conferred advantages to the system I was mutating. On rare occasions an instability has shown up under very specific conditions, as you mention. I would then revert to a previous version, or make an additional mutation for the specific conditions.

I was able to do all this in spite of not having read all of the INCOSE literature. How is that even possible?

If a genetic mutation would have such side effects, the theory of evolution predicts that negative selection would likely remove it from the population. Meanwhile, positive selection would likely fix a positive mutation in the population.

This is not just hypothesizing or circular reasoning. Biologists have identified thousands of specific mutations and corresponding positive (or negative) phenotype changes.

Blessings,
Chris


(Raymond Isbell) #360

Randy,
Not sure why I missed this link (https://discourse.peacefulscience.org/t/rumraket-response-to-dr-tour-on-abiogenesis/4242/3 from your post #234), but it looks to be interesting, and since I like to see both sides of an issue, I plan to spend some time reading it. Thanks!


(Raymond Isbell) #361

Did you watch the video? It’s absolutely about evolution and abiogenesis. Tour sees the same problem with both, viz., “What’s the mechanism?”

It’s interesting how you guys seem to only capture facts as they relate directly to this argument instead of a deeper understanding of the underlying issues. You seem to be more interested in winning the argument (viz., what’s the better explanation for life, evolution or design) as exemplified by your various approaches (e.g., challenges of my knowledge of biology) rather than the real issue which is my effort to explain the inference of SE on evolution which is a subset of Tour’s concerns, i.e., what’s the mechanism. SE sees significant difficulties in any chance mechanism that can explain evolution. In this regard, Tour and I have a common concern.

This is a classic “red herring.” You know full well that I don’t expect or require omniscience. Omniscience is not a necessity. Abductive reasoning, however, is.

Incidentally, I happened upon this website this morning that was interesting and completely consistent with the image that’s forming in my head about evolution. It illustrates my concern over the weak foundational evidence adduced by evolutionists for their theory. https://www.youtube.com/watch?v=lIEoO5KdPvg&lc=z22qcjrrtx2fc5nzq04t1aokgcsvpzh3tztz35dofpu2rk0h00410

the segment on Cetaceans was clearly full of extrapolation and eisegesis. I find presentations like this to be troublesome in that they present only one side as though it was proven fact. They fail to note that substantive arguments against this view are held by responsible scientists such as Tour, Meyer, Denton, et al. What’s the harm in presenting a counter view and suggest that viewer do some individual critical thinking before deciding. That’s one significant problem with evolutionists. They present their side as proven and accepted, and mock alternative views as only being embraced by extremists such as flat earthers. If we’re all seeking the truth, why is there suppression of the ID and Creationist narrative? Wouldn’t all be better off in the long run if the both sides encourage open and respectful debate. If evolution turned out to be the best explanation, it would rise to the top and become clear to all. Unfortunately, the evolution sides actively try to suppress its opponents as though they had something to hide.

What say you?


(Raymond Isbell) #362

What you’re leaving out is the qualification that the evidence adduced for these thousands of specific mutations and corresponding positive (or negative) phenotype changes supports only micro-evolution, not macro. There are no obvious examples of macro-evolution that don’t first require a lot of unproven assertions by loyalists to the evolutionary camp. Why not provide a SE argument that shows the step by step progression from the original mutation, and its successors to the many protein changes in the cell both individually and collectively (e.g, tissues, organs, etc) on up to the specific phenotype structural and functional changes that constitute the new species? And don’t forget to describe the “mechanism” (See Tour). The reason you don’t is that you can’t. Thus, you’re back to the only arguments you have supported by evidence which is characterized by “is consistent with” and “may account for.” That narrative leaves open the significant possibility that evolution is a dog that won’t hunt, and that your belief in it is really a faith system, not a scientific one. Can you be honest enough to admit that or will you claim that critics just don’t understand biology, (e.g., Tour, Denton, Meyer, Wells, Demski, Berlinski, et al)