Reaping the Whirlwind: protein function without stable structure


(Chris Falter) #383

Another example of a theory that should collapse under the weight of Isbell’s logic is plate tectonics.

Sure, we have evidence of micro-plate tectonics from GPS measurements. But macro-plate tectonics and Gaia are a different matter altogether. You would have to show exactly much crust got subducted, when, and where, to give a complete description of the mechanisms that supposedly led to the formation of the San Andreas Fault. Geologists cannot do that, therefore the macro theory of plate tectonics is just speculation and circular reasoning.

Now an Isbellian thinker would be fair, as Isbell is, and concede that geologists have described much evidence that is consistent with macro-plate tectonics and Gaia. Topological symmetry between the west coast of Africa and the east coast of S America. Matching fossil communities in matching layers on the two coasts. Fossils of sea creatures at very high elevations today.

But these are only consistent with the hypothesis. We demand a higher standard: all mechanisms and interactions over hundreds of millions of years must be described in full detail in order for the hypothesis of macro-plate tectonics to be accepted as a scientific theory.


(Chris Falter) #384

Do you know of any branch of science that does not use extrapolation?

I would be curious to see, Raymond, if you could name just one branch of science that does not use interpolation or extrapolation. Just one. I cannot think of any.

As for eisegesis, what would the null hypothesis be? The evidence is that a succession of fossils, when ordered chronologically, shows a slow, gradual change in features: nostrils to blowholes, front legs to fins, etc. The null hypothesis would be that in spite of their remarkable similarities and chronologically ordered sequence, the fossils that give a strong appearance of gradual feature evolution between intermediate forms are not in fact related to one another.

But consider: we consider narwhals and blue whales and orcas to be related in spite of noticeable differences. Is the family relationship of various modern cetaceans just eisegesis? If not, then neither should we regard relationship between fossil species of cetaceans to inherently be eisegesis.

This is particularly true because of evidence from genomic sequence data. However, not once in this conversation have you even shown any awareness of genomic sequence data, if memory serves correctly. But here’s the thing: mathematical models of genomic data show that the nested hierarchy of mammals is the best explanation to an extremely high degree of confidence. Mathematical models of phylogenetic traits reach the same conclusion. And both of these are in agreement with the evolutionary modeling of fossil evidence.

When multiple independent lines of evidence support the same theory, each one with a high degree of confidence, then the scientific community tends to accept that theory.

As long as you exclude mathematical analysis of genomes and traits from your consideration, Raymond, you will be tempted to think that evolutionary explanations of fossils are eisegesis. But there is good news: With some intensive reading you can gain a rudimentary grasp of the mathematical models that have treated genomic and trait characters.


(Dennis Venema) #385

Raymond, I find it curious that you have, on several occasions now, not grappled with genomics evidence for evolution when it is presented to you. I presented a specific type of genomics-based evidence, and tried to explain it clearly.

Are you willing to engage on this evidence?


(Raymond Isbell) #386

It’s an analogy to show the unlikelihood of a cell self-assembling from non-organic chemicals. Most people do not have a feel for how unlikely it is. The analogy puts a face on it. I suspect that the reason it gives you disquiet is because it forces you to face the reality of what you believe. And I’m not just talking about abiogenesis. I also believe it applies to evolution of living cells where new and novel structure and function arises such as is the case of a land going creature like a hippo evolving to a sea going creature like a whale. The list of structural changes at the phenotypic level is impressive. The lower level changes in organs, tissues, cells, and proteins is probably even more dramatic, not to mention the command, control, communications, and computing (C4) functions. To believe that evolutionary changes can account for this suggests that one understands how it happens, i.e., what is the mechanism at a sufficiently low level of detail that makes it credible where bias extrapolation can you rule out? (By the way, how do define the threshold where biased extrapolation can be distinguished from unimpeachable scientific data?) If you’re intellectually honest, you must admit that you’re doing some heavy extrapolation. After all what evidence do you have? A set of pictures of fossil bones that could have many interpretations, and what one would expect to see at a sixth-grade science fair’s show and tell? And yet you claim that this is solid confirmatory evidence for macro-evolution. Really?

Since you brought up the probability issue, let’s address that. I’m sure you all are aware of the model offered by the ID folks where they calculate the probability of a functional amino acid sequence (any useful function to the cell) with 150 amino acids in length. The estimate is built on 3 facts, and includes an adjustment up that reflects Doug Axe’s consideration for those sequences that are functional. The 3 facts are:

  1. Given there are only 20 amino acids that tie back to the DNA codons (standard amino acids) (See, I’m learning some biology!), those 20 can be arranged in 10^195 possible ways. (Simple math)
  2. Amino acids can only be the left-handed variety (chirality) (1 in 2 chance of happening) which for a sequence of 150 amino acids, that adds another factor of unlikeliness that can be calculated to be 10^45 (simple math).
  3. The amino acids must be bonded with a peptide bond which also has a 1 in 2 probability. That adds another factor of 1 in 10^45.

Conclusion: From just the math for a 150-chain amino acid sequence, the probability of any sequence (functional or not) is the product of these 3 probabilities, or 1 in (10^45 x 10^45 x 10^195) or 1 in 10^285. Now let’s consider the adjustment necessary for the presence of functional proteins, not just any protein.

To finish the calculation for the probability for a single functional protein 150 amino acids long, we have to adjust up the smallest number of 1 in 10^195 which is the number of possible amino acid sequences using only 20 amino acids to account for the fact that many of these sequences may have function in the cell. We can consider a lower bound on this number from Doug Axe in his JMB article as 1 in 10^77. We can get an upper bound from the calculation provided by an evolutionist named Arthur Hunt at (https://pandasthumb.org/archives/2007/01/92-second-st-fa.html). That website is devoted to supporting the evolution narrative. (Our friend Rumraket who toys with reality makes many generous assumptions as I said earlier that are highly questionable. But let’s take one of his numbers using those assumptions, viz., 1 in 10^3. (I didn’t include his many assumptions of various peptide bonds already existing, because that violates the model’s definition.) I might also add that Axe’s number was cleared by the referees of JMB. Thus, it carries some authority unlike Rumraket.

Thus, a lower bound on the probability is estimated at 1 in 10^167 using Axe’s number. The upper bound would be 1 in 10^93 if we used the number proposed by Rumraket.

Finally, as I’ve said before, this estimate is way too low if you consider the SE requirements where changes must be made in synchrony with others if the cell is to remain viable. I’m sure you will reject this last statement, but that’s because you don’t understand SE in a complex systems. Also, it’s not that you don’t understand because you don’t understand. It’s because you refuse to accept it. It doesn’t fit your narrative, so you won’t let it in. I don’t know how to fix that. Also, I don’t think this is a strawman. That’s an easy way out of an argument you haven’t won on the merits of your logic.


(Raymond Isbell) #387

For sure. Are we going to set some rules for what constitutes scientific evidence? Will evidence be characterized and classified according to good scientific laws and principals? Let’s work on that so we can both agree. This applies to Chris’ concerns on extrapolation being acceptable in many scientific disciplines. I agree that extrapolation is useful. But it must be done so carefully in specific contexts. Good extrapolation is always qualified so that gratuitous extrapolation isn’t allowed.


(Chris Falter) #388

You are making an argument regarding abiogenesis here, Raymond. As I and many others have mentioned previously, this has nothing to do with the theory of evolution.

It’s worth bearing in mind a couple of things:

  • Axe’s peer-reviewed paper was conducted within a particular set of conditions. Outside of those conditions, the estimate of 10e-77 has not held up.
  • I have not seen Rumraket’s estimate of 10e-3. I have seen Art Hunt’s estimate of 10e-10, which was published in a peer-reviewed article. Hunt’s experiment obviously explored a different set of conditions than Axe’s.

I have never seen probability calculated in this manner, and I believe you must have overlooked something. The lower bound using Art Hunt’s 10e-10 estimate in conjunction with the chirality and peptide bond factors would be 10e-(10 * 2 * 2), or 10e-40. The lower bound using Rumraket’s 10e-3 would be 10e-(3 * 2 * 2), or 10e-12.

Sure, evolutionary biologists have a “narrative,” aka the theory of evolution. It also has explanatory power over a wide variety of evidence classes, and has made innumerable predictions which have been confirmed by observation.

But I should bear in mind that you are discussing abiogenesis, which is not part of the theory of evolution…

How about yourself, Raymond? Are you narrative-free and bias-free?

The ball is in your court on this question, Raymond. How it is that you do not even realize that, I do not understand.

I remind you that I argued at great length that your approach to any branch of science that deals with natural history (geology, solar system astronomy, astrophysics, biology) is at odds with the practitioners of those scientific disciplines.

I find it very, very odd that you would implicitly demand conformance with your views of how science should be done when someone who cares deeply about you and about the science has already made an extended argument about how science is and should be done.

If you would like to discuss scientific principles and procedures, may I suggest you reply to those posts of mine?

Yours,
Chris Falter


(Mervin Bitikofer) #389

Not only do I not have a “feel” for abiogenesis, I don’t even understand it at all. Theorists are still trying to build theories on that - and so lay people like you and me are certainly in no position to understand the possibilities there, much less evaluate their likelihood.

But evolution (what I thought we were discussing here) is a whole 'nother story. Sure, there are lots of ongoing areas of investigation there too, but the core of the theory has proven amazingly robust. As Chris writes above, there are actually quite a few “un-returned balls still in your court”. All I’ve seen from you is the charge that your engineering approach is not able to make sense of the theory, and therefore you think the professional biologists and their long-developed methods and theories must be where the problem is. I think I’ll stick with the professional assessments of the insiders rather than the outsider who has repeatedly demonstrated a lack of understanding of what evolution even is.


(Raymond Isbell) #390

You should have read the next sentence where I said, “_I also believe it applies to evolution of living cells where new and novel structure and function arises such as is the case of a land going creature like a hippo evolving to a sea going creature like a whale. The list of structural changes at the phenotypic level is impressive. The lower level changes in organs, tissues, cells, and proteins is probably even more dramatic, not to mention the command, control, communications, and computing (C4) functions.” This means that if you bring yourself to think like an engineer who recognizes the concept of interdependence, then you would recognize that I see abiogenesis as possibly less demanding that a large number of coordinated changes necessary for a cell to move from one level of function to a new one. I am aware that you claim changes accumulate via evolutionary capacitance for instance so that the likelihood of moving to new function is easier. Problem is that neither you nor anyone else can show conclusively that that is what is happening when you see new function suddenly appear. How could you when you don’t even understand the mechanism? How can you model and test for a function that you don’t know completely its composition, e.g., the gene/alleles, the proteins and their folds, how that fits into the next series of higher levels of function all the way to the phenotype? Can a test be considered valid if you don’t know the workflow and how each of the components interact and respond to unknown inputs? For these unknown components (proteins), do you know their transfer functions and intermediate states that may depend on other conditions? You have no clue. Neither does anyone else. This is the part that is amazing to me. There’s so much in the cell that you guys have no clue about their function(s), dependencies, the role they play in higher level processes, etc. How can you possible assume you know enough to conclude that evolution is the mechanism? Your confidence in evolution is built on narrative that comes from observation of such a small subset of the total suite of functions, that it can hardly be said to be scientific. A good scientist first recognizes his/her limitations. (Clint Eastwood!) Isn’t it interesting that both Axe and Hunt have published peer-reviewed papers and they have different conclusions. Doesn’t that tell you something?

It’s in the link I sent where I referenced Hunt’s number. That link was written by Rumraket. He used Hunt’s number to reinforce his narrative.

Is that a statement of “personal incredulity?”

Does Stephen agree?

Of course not. But remember, I’m playing the devil’s advocate and taking the position of ID for arguments sake. Here’s your chance to defend evolution (if you can).

Since at bottom we’re both looking for the truth, shouldn’t we both obey the same rule set? And shouldn’t we work to agree on what that rule set is? I’m Ok with taking the lead and proposing something. A good starting point would be, "When is extrapolation valid, i.e., what criteria is needed to show that an extrapolation is valid. I don’t think that is possible with the current fossil record for the problem of land mammal to cetacean. But we can work on it to see if some enlightening is possible.

Strange that I’m seeing in the biology literature I’m reading that systems engineering is starting to show promise and add clarity to the problem. In fact I included references to it just recently.

Strange again. My views about how science should be done are mainstream, universally practiced by engineers who build things. Of course if cell biology has a different set of laws and principals, then I stand to be corrected. Please point to those posts and I’ll take a second look.


(Dennis Venema) #391

By the way, it’s “principles”, not “principals”. Sorry. /pedant

What I shared with you was simply what we can observe in nature. These facts are not in dispute. As such, scientists seek to explain why these undisputed facts are the way they are. I was asking for your explanation of these observable facts:


(Stephen Matheson) #392

Of course. Everyone does. Abiogenesis is not, by definition, part of evolutionary theory. That’s as basic as ABCs.


(Chris Falter) #393

Hi Raymond,

No, I was trying to say in a gentle manner that you botched the probability calculation. And you did, by astronomical orders of magnitude.

I am gasterflabbed. I gave a simple derivation of the correct application of probability theory to our discussion. Then your response was a complete non sequitur, and did not even attempt to address the derivation. What kind of discussion is this? Instead of interacting with the substance of my arguments, you seem to be trying to score rhetorical points.

Chris: Your framework for scientific theories of origins is at odds with well accepted theories in many branches of science.

Raymond: Systems engineering is helping biologists understand cellular structures better.

Again, your response is a non sequitur. The appearance is that you are trying to score rhetorical points rather than interact with the substance of my arguments.

I gave a very detailed argument for inference to theory in a variety of natural sciences, but you completely ignored it. Instead, you said, “Hey, look at my favorite subject!”

This statement is an oxymoron on its face. Engineers are marvelous people and they do marvelous work–engineering. It is not by a very long stretch the same thing as science. The disciplines certainly interact, but they are very different disciplines.

You have been ignoring every criticism of your choice to focus on a very narrow set of SE principles. Hundreds of posts ago you did not understand the most fundamental tenets of microservice architecture, yet you insisted that my criticism of your statements was personal invective. Thus you still do not seem to understand how microservice principles–a different subset of SE principles–provide a very evolution-friendly view of how changes can be introduced into complex systems. You did cite an INCOSE statement to the effect that microservice architecture does not eliminate complexity, but I have never contended otherwise. What I have asserted is that microservice architecture is orders of magnitude more robust to incremental change than monolithic architecture. The evidence for my assertion is the rate of change at Amazon and Netflix.

You also showed zero interest in how the mathematical dynamics of neural networks, another form of system engineering, can provide insights into biological evolution. I invited you to ask questions, and your response was…crickets.

Your intense focus on a subset of SE principles to the exclusion of other highly relevant SE principles leads me to believe that you are not willing to take account the ideas that I am trying to introduce to our discussion. I’m sorry that I have had to reach this conclusion, Raymond. But note well: The conclusion is based on your behavior in this thread.

Clearly you did not read my LinkedIn profile.

I already answered this in posts #382 and #383, and I do not care to repeat myself. If you are interested in having a conversation, I invite you to read those posts and respond to their content.

Go back to all the issues I and Dennis Venema have raised that you have chosen to ignore, and address them. Then I will know that you are sincere in pursuing a true exchange of ideas, and we can continue.

I already addreesed the issue of multiple classes of evidence in post #385 and I do not care to repeat myself. If you would like to have a conversation, I invite you to read that post and respond to its content.

More importantly, your statement is an extraordinarily ungracious thing to say about tens of thousands of scientists–thousands of whom are brothers and sisters in Christ–who have devoted their lives to a scientific oeuvre that you have studied very little.

And no, studying the criticism of their work does not qualify as studying their work. I am not saying you should never study the critics. I am saying you should put Proverbs 18:17 into practice. Silence the voice in your head that is shouting “But SE!” for a while (not forever) as you read some books by evolutionary biologists.

When all is said and done, have a blessed day, my brother.

Chris


(Raymond Isbell) #394

Good catch. I could blame my spell checker, but it’s likely that I was just in a hurry and didn’t give it the scrutiny I should have. I must be wrong on evolution as well! :grinning:

When I see test results that seem to be simple and what I would expect, I usually hear a voice in the back of my head saying, "Be careful. Have you considered other effects, relationships, downchain consequences that may not appear immediately, etc., that you haven’t anticipated? Was your testing such as to ensure it was a good test designed carefully and thoroughly so that bias doesn’t come into play? Good testing is first and foremost dependent on the test designers knowledge of the system being tested. In the case of the cell, can you really claim a test result with high confidence given that you don’t have a full understanding of cell, its component interrelationships, downchain impacts of change, etc.

I stumbled upon this video that is an interview of David Berlinski commenting on the significant weaknesses of the Darwinian model. (https://www.youtube.com/watch?v=S89IskZI740) What I noticed was that he sees many of the same things that I see and have been trying to communicate to you guys that you don’t seem to be catching. Perhaps his explanation might be better than mine. Watch it and see if you can keep an open and objective view as you watch it.

You guys insist that I’m not listening/reading the materials that you send me. Not true. I read them, and realize that they are really disguised attempts to justify your biological eisegesis and unjustified extrapolation, e.g., the land mammal to whale story.

Extrapolation works well when the relationship between points is linear. What if the relationships are higher degree and thus, non-linear? How can you show that your extrapolation is justified in that case? Where is your error analysis and budget? Have you considered other models such as design. We both know the answer. The simple fact is that you don’t know the cell well enough to build a scientifically developed and sufficiently complete error map that links error estimates back to assumptions and model variables. That’s why you resort back to simple testing with many unjustified assumptions that will verify questionable predictions based on inadequate modeling of the process. If you believe your test models are adequate and can show certainty for your conclusions, please explain how that can be done with current understanding of the cell. You’ve said that certain aspects of the cell are well understood. If so, that would mean that you have established all the relationships between all the proteins and their linkage back to the genes/alleles. Is your knowledge of the cell that extensive?

Neither evolution nor design can produce a provable set of tests. That’s why we resort to abduction to draw a conclusion. That conclusion should be tempered with the knowledge that we really don’t fully understand the cell and thus we should be open to change as more data is captured.


(Raymond Isbell) #395

What do we call this? A classic strawman?

Slow, gradual change? Really? There’s an extraordinarily large number of coordinated genome and accompanying phoneme changes needed to get from nostrils to blowholes, front legs to fins, etc. See this article at the Evolution News website on the land mammal to Cetacean transition. (https://evolutionnews.org/2018/07/from-bears-to-whales-a-difficult-transition/) It will show that your description above is deceptively simple, and reflects a puerile approach to understanding the data. This is a classic example of unjustified extrapolation and eisegesis. I don’t think you could have done a better job of undermining your position than this quote.

Are these models that reflect a thorough understanding of the mapping of genes to proteins to phenotypic traits verified to be complete and correct? (See my recent post to Dennis.) A model by an evolutionist design to show the truth of evolution?

Independent lines of evidence? Really?

You really need to qualify the kind of mathematical analysis of genomes and traits that I exclude. That, of course, is the kind that I see coming from the ranks of evolutionary biologists and other proponents of evolution. I think I’ve said enough about their qualification to be call scientific. Watch the Berlinski video: https://www.youtube.com/watch?v=S89IskZI740 It should help you to understand what I’m saying.


(Raymond Isbell) #396

Actually, I didn’t. The problem is that it doesn’t fit the evolutionary narrative.

I saw an incoherent claim of some combination of Hunt’s and Rumraket’s numbers. I didn’t see anything original from you, just your selectively and with bias choosing Hunt’s model and pretty much ignoring the chirality and peptide bonding factors. Rumraket as as I said before is detached from reality so it’s hard to find credibility in anything he says. If he were supporting my side of an argument, I would be concerned. If you have a good stochastic model that is credible for evolution, I would love to see it. Please send a link.

“Systems engineering is helping biologists understand cellular structures better.” is a non-sequitur? Huh?

If careful logic is just a rhetorical point, then “Houston, we’ve got a problem.” I don’t know how to answer that. Regarding the substance of your arguments, is the statement “slow, gradual change in features: nostrils to blowholes, front legs to fins, etc.” an example? That’s oxymoronic! You need to work on your understanding of the term “substantive.”

The term substantive will aid greatly if we apply it to evidence such as the fossil record. We know it’s discontinuous, that’s a fact. It may get better, but they’ve been saying that for a long time. Phillip Johnson says about the fossil record in his book “Darwin on Trial,” “In short, if evolution means the gradual change of one kind of organism into another kind, the outstanding characteristic of the fossil record is the absence of evidence for evolution.” He quoted Stephen Gould, "The history of most fossil species includes two features particularly inconsistent with gradualism: 1. Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking pretty much the same as when they disappear; morphological change is usually limited and directionless. 2. Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and “fully formed.

Let’s strive to be substantive.

One final point that I found odd. You claim that I haven’t looked at your Linkedin cv. I did and noticed that you’re not trained in the physical sciences. That may explain why you have difficulty understanding SE. An undergrad degree in engineering gives you good exposure to math, physics, chemistry, mechanics, electro-magnetics, fluids, gases, system dynamics and material science. The best class I ever took was system dynamics (Engr 104 at Stanford) taught by Robert Cannon, the man who designed the inertial navigation system for the Apollo program. That class took all your knowledge from the other engineering disciplines and taught you to integrate and model various combinations of them. The models were linear so they had limits, but the study of those limitations was my first exposure to complex physical systems. It gave me a deep appreciation for things that you seem to gloss over.


#397

Problem being it has been getting better for a long time. The fossil record for whales and horses being two examples.

More like misquoted. This is a classic quote mine of Gould often used by ID/Creationists. What is left out is this little snippet.


(Raymond Isbell) #398

I think you would have been better off to have not said that. Notice the quote I used states facts/conclusions by Gould. The quote you used states wishes (should yield). Good for Gould. He was honest enough to distinguish between what the fossil record shows, and what he thinks it show. Would that all evolutionists had that kind of honesty!


(James McKay) #399

Does anyone have a source for the full quote, in context?


(Matthew Pevarnik) #400

Either you did or didn’t. Which is it? Either way, that has no bearing on the theory of evolution. I’m not sure if you realize that scientists aren’t in the business of just making stuff up as this thread began with an example of you making up a scenario that was completely wrong to begin with.


(Raymond Isbell) #401

Can you provide a pointer to that? (Post #) Was it wrong or did you guys just not like it?


(James McKay) #402

No Raymond, it’s important that he did. If you’re quoting people, it’s essential to make sure that your quotes accurately reflect the context in which they are said.

Rightly or wrongly, creationists and ID proponents have a reputation for quote mining. The only legitimate way to counteract that perception is to be scrupulously accurate and transparent in quoting people. That means providing direct links back to the original source.