Reaping the Whirlwind: protein function without stable structure

(Raymond Isbell) #182

An engineering approach works anywhere there are physical laws in operation. You and others seem to be suggesting that other forces and laws are at play in the cell. Dennis has suggested that cells can respond to variations in molecular structures just as one who listens to a foreigner speaking a different language can understand some of it, and with time will adapt to understand most if not all of it. I think this where our disagreement is becoming understandable to me. In my mind everything going on the cell is physical in nature and therefore must obey physical laws. SE works well when describing systems like that. it sounds like in the minds of EC advocates there’s more going on in the cell than obedience to physical laws. Are ya’ll really saying that? That would certainly explain what I’m hearing that has me scratching my head. What do you call these other forces beyond mechanics, electro-magnetism, etc?

Yes, I’m assuming the cell is a complex system that obeys all the physical laws of the universe. All that SE does is describe how a system employs those physical laws to achieve some mechanical/electrical/chemical function.

No disagreement. I’ve actually been trying to make that case. Sounds like I’m not doing very well. Also, it never entered my mind to hold Steve accountable for failure/success of EC. This is an academic discussion. I don’t have any opinions about persons who hold different views than my own. I’m seeking to understand their thinking.

No argument from my quarter.

I agree. What I’m trying to understand is how you can conclude that this fault tolerance we’re observing can come about by chance. To me it requires very careful design. The cell illustrates how well it works, and how smart the designer is.v

(Stephen Matheson) #183

That is the topic of lots of interesting research, some of which I know very well. I doubt very much that the particular SE view that you prefer would be helpful in this pursuit, but no cell biologist would hesitate to avail herself of new tools or viewpoints.

A deeper understanding of cellular functions and systems is not how we would decide about whether evolution works as an explanation. All thinking scientists want to avoid the Argument from Ignorance and the Argument from Personal Incredulity, so merely describing the extraordinary complexity and the design principles evinced by a cell just won’t answer any evolutionary questions. It can motivate the questions, and it does, but it can’t answer them.

No, we don’t know that, because that’s false.

You are describing the discipline of cell biology, and its interfaces with molecular genetics and systems biology. These are robust research areas, to which whole journals are devoted, including journals whose editors are my closest friends and colleagues. Your questions are great. But you seem to assume that no one has thought to look at them. I don’t understand why.

That’s what you think of the numerous papers that have been cited in this conversation? You have read the literature on cell biology and think that is “hand waving”?

I have a suggestion. Consider discussing biology, from your interesting engineering perspective (in fact, your viewpoint is interesting and potentially useful), and consider casting no further aspersions on the people here. Maybe you can’t see how contemptuous it is to suggest that biologists have something to hide, or to suggest that review articles describing and quantifying robustness are “hand waving”, but it’s really not a good approach.

(Mervin Bitikofer) #184

I don’t think anybody here would take issue with that.

Well -that following sentence seems to me like a sweeping claim that doesn’t necessarily follow from the prior thought. Most of us here (believers and otherwise) would agree that everything that ordinarily occurs in nature “must” or does follow physical laws. My interactions with my students in my classroom could be seen as just such a physical “system”, if you will. But I doubt that anyone would find systems engineering approaches to be of much use to help one strategize and navigate their day of interactions with a diversity of students and families. You may have a very shiny hammer indeed, but it does not follow that “physical processes” = “nothing but nails”.

(Dennis Venema) #185

What I am offering you is an analogy to try to help you understand why biological systems are not brittle in the way you think they must be. It’s an analogy, not a physical description of how cells work.

The points of the analogy:

Both languages and the proteins undergirding cellular functions have variation within them.
Both systems have a process of population-level, incremental change over time that produces standing variation.
Mixing and matching that standing variation in new combinations is usually fine. Not always, but usually. We can observe this in both systems.

Ergo, if you think that changes to any part of a cell’s components must be coordinated in order to avoid catastrophic failure then you don’t have a good understanding of what is already well-known by biologists. You might not know this about cells, but I’m hoping you can understand why a language (a system with which you are more familiar) will not suffer catastrophic failure if changes occur (over time and space in different populations). The idea is that the analogy might help you see how (in principle) a complex system might be resilient to change even if you don’t know the underlying points of correspondence to biological systems.

Ok, I feel like I do when I’ve just explained a joke… :slight_smile:

(Raymond Isbell) #186

I definitely see the analogy, but the problem is that physical systems and abstractions reflected in language are material and non-material respectively. Not a good way to convey your point via analogy. Material things obey the laws of physics. Non-material things do not.

Advocates of EC press the point that Cells are not brittle. I can accept that, but the reason Cell processes exhibit resistance to brittleness is because they incorporate Fault Tolerance (FT) functionality. (You call it RFR which are simply descriptors of FT). I’ve tried to stress that FT is very unlikely to happen by chance. Design seems to be a better explanation. There are many peer reviewed publications in IEEE on the subject of FT. It’s a hot topic in those circles.I wonder if cell biologists are reading the IEEE publications on it. It might give them some ideas on research strategies. FT is a hugely important function that is integrated into mission critical systems. It works with physical laws and is measurable and quantifiable. Nothing non-material going on.

I feel like I’ve had to explain FT over and over, and it’s not getting any traction. A well designed system with FT will exhibit robustness, flexibility, and redundancy. The difference we have is that you see it as an argument to support EC while I see as an argument against EC and for design. The reason is simple. FT systems are far more complex and more difficult to change because of the high levels of interdependence between the Cells many sub-functions.

(Christy Hemphill) #187

But living things aren’t machines. Don’t you think there is something “immaterial” about life?

If physics was sufficient for describing life, why do we even have biology?

(Dennis Venema) #188

I’m not really defending EC per se here (though yes, I do hold to an EC view). This is just standard biology.

I’m sure you have a better understanding of FT in systems engineering than I do, but I don’t think you understand why biological systems can tolerate changes in the way they do. If you did understand it, I think you would see that the reasons are very compatible with evolution. But that will take some effort on your part - just like it would take some effort on my part to speak knowledgeably about engineering.

(Stephen Matheson) #189

Mitotic-Exit Control as an Evolved Complex System

Abstract: The exit from mitosis is the last critical decision during a cell-division cycle. A complex regulatory system has evolved to evaluate the success of mitotic events and control this decision. Whereas outstanding genetic work in yeast has led to rapid discovery of a large number of interacting genes involved in the control of mitotic exit, it has also become increasingly difficult to comprehend the logic and mechanistic features embedded in the complex molecular network. Our view is that this difficulty stems in part from the attempt to explain mitotic-exit control using concepts from traditional top-down engineering design, and that exciting new results from evolutionary engineering design applied to networks and electronic circuits may lend better insights. We focus on four particularly intriguing features of the mitotic-exit control system and attempt to examine these features from the perspective of evolutionary design and complex system engineering.

(Raymond Isbell) #190

I would say that living things are hybrids, i.e., both physical machines and immaterial “life” (soul and spirit). God has integrated the two. Atheists must attribute abstract thinking and reasoning, not to mention emotions, to physics and chemistry. From that perspective, I wonder at what point some combination of chemicals starts to perform abstract thinking? One from the readership of this group referred me to a concise article at that provides a nice summary of systems biology where biology and systems engineering are recognizing they are related.

As it relates to my being here in the first place, I’m looking at it to help me resolve whether EC is more or less compelling that ID. Currently in my mind, ID has the lead, but I want to make sure I understand EC before I rule it out. The article at the Britannica link above provides an excellent summary perspective of biology and systems engineering. One quote is worthy of mention,

“A comparison with systems engineering can provide useful insight into the nature of systems
biology. When engineers design systems, they explore known components that can be put
together in such a way as to create a system that behaves in a prescribed fashion, according
to the design specifications. When biologists look at a system, on the other hand, their initial
tasks are to identify the components and to understand the properties of individual
components. They then attempt to identify how interactions between the components
ultimately create the system’s observable biological behaviours. The process is more closely
aligned with the notion of “systems reverse engineering” than it is with systems design

(Raymond Isbell) #191

Sounds like you’re saying that if we understand less, we’ll know more. Huh? (I’m shrugging my shoulders.) Further into this post you suggest (good suggestion) that I stop casting aspersions on people. I thought I was challenging ideas, not people. If I did, I apologize. In this regard it’s hard to not notice the pejorative labels you cast in my direction, e.g., “all thinking scientists,” “Argument for Ignorance,” “Argument from Personal Incredulity,” etc. Stepping back and looking at it, you seem to be taking my challenges personally. Let me assure you that I am not. You’re clearly intelligent and learned. Unfortunately, that makes you a nice target for the challenges I put forth to see if EC or plain evolution is a good explanation for the Cell. But it’s not personal. My position is that the Cell obeys physical laws, and as such SE is helpful tool to use to increase our understanding of cell function. (I see understanding and knowledge as highly correlated.) In a real sense, I’m saying that if we reverse engineer (systems engineering) the cell it will increase our understanding of cell components along with their functions and relationships to other cell components and eventually lead us to make an informed judgment (abductive reasoning) about whether EC or ID is the best explanation of the Cell. Since mankind (you, me and everyone else) has a long way to go before we fully understand the Cell, it means we should be careful before we abductively decide that EC or ID is the best explanation. You seem to have already made up your mind. Recommendation: Let’s stop the personal attacks in keeping with the guidelines of this forum, and make a positive contribution. Let’s be helpful, not antagonistic. If you find my ignorance of biology offensive and not worthy of your time, you can easily not contribute at all. I learn quickly, and am motivated to get to the point where I feel confident about either EC or ID. (I will admit that I’m wrong when the evidence becomes overwhelming against me, but so far, I’m not seeing it. You can help me get there, or you can keep taking cheap shots at me. If the latter, I’ll simply filter out the negative and try to use the positive. I won’t ignore you. You’re a valuable resource. It’s far more important to me to understand so I can make an informed decision rather than winning/losing an argument with you.

By the way, thanks for the reference. I find this quote from the abstract intriguing: " Our view is that this difficulty stems in part from the attempt to explain mitotic-exit control using concepts from traditional top-down engineering design, and that exciting new results from evolutionary engineering design applied to networks and electronic circuits may lend better insights." Skimming thru it, it looks to be a really good read, and I look forward to spending some serious time with it. I appreciate you providing it. You’re a good man…I don’t care what they say!

(Chris Falter) #192

I read the same text as you, and came to the opposite conclusion. If I am understanding him correctly, Steve is saying that the complexity of biological mechanisms gives us a choice:

  1. Label it as intelligently designed and admire it, or
  2. Inquire further into the origin of the mechanisms using the scientific study of biological origins.

He is urging choice #2.

(Raymond Isbell) #193

But here’s what he said: “A deeper understanding of cellular functions and systems is not how we would decide about whether evolution works as an explanation.” Are you’re saying he doesn’t mean it? That’s possible, I suppose. I expect that he wrote it quickly and didn’t proof it before he release it. From my viewpoint, understanding of cellular functions and systems is exactly what is needed to make an informed decision about whether EC or ID is the best explanation. SE is an excellent tool to help us gain that understanding. Your point # 2 suggesting that we inquire further into the origin of the mechanism using the “scientific study of biological origins” is the correct way is puzzling. What is the “scientific study of biological origins?” If it’s doesn’t take us to a deeper understanding of cellular functions and systems, what value is it? Can I possibly make a judgment about the origin of something if I don’t understand how it works? I’m clearly missing something!

(Dennis Venema) #194

I have only a little understanding of how the Spanish, Italian and Portuguese languages work, but comparing them makes it plain to me that they are related to each other. Similarly, when comparing the DNA sequences of chimpanzees and humans it quickly becomes apparent that the hypothesis that they are relatives is very, very strongly supported - even if we do not have a full accounting of every function.

(Stephen Matheson) #195

My words, and your interpretation, are so different that I can only tell you that your failure to understand me is your problem and not mine. What I wrote, which I think is quite clear, is that our increasingly detailed understanding of how systems work is not how we would decide about whether evolution works as an explanation. The question of whether evolution works is answered by considering whether and how it can explain how that system got to be how it is. Those are fundamentally different questions, and that is a very basic concept.

You have made your goals very clear. I know this is what you want to do. I think it sounds great. It’s not a new idea, not at all, and it doesn’t seem that you are proposing new approaches or angles. But you are right that reverse engineering has the potential to provide new insights into how things work, and potentially into how they evolve and evolved.

There are two ways we disagree here. One is with the separation of evolution and design. (I won’t use the term ‘EC’ because that describes a religious position and not a scientific view.) I think it is an error to ask whether “ID” is true to the exclusion of evolution (descent with modification). The most well-known ID proponent in the world (Behe) doesn’t make that distinction. For me personally, the existence of design and the questions raised in the context of design are very interesting, highly relevant to understanding biology, and unanswered. But they have no necessary connection to evolution or even to Darwinian emphases on “random” mutation. My unfulfilled desire on Biologos is to find people who want to go deep on the notion of design, without all the baggage of culture war, creationism, and nonsense. (It’s just my personal obsessive interest. Biologos isn’t really the place for it, and in my life now isn’t the best time for it.) So, for me, your apparent insistence on setting up “ID” as an alternative to evolution is a no-go. Not logical, not interesting.

The bigger disagreement is with your apparent conviction that merely describing the complexities of cell biology will lead by itself to a conclusion about evolution versus “ID”. This is false, as I explained above.

It’s more complicated than that. About ID creationism, I have made up my mind. It has no explanatory value. The best it can do is create gaps for gods to fill, and it is usually based on errors like the Argument from Ignorance and the Argument from Personal Incredulity. (These are informal terms for big logical errors. They are not insults.) And I have made up my mind about common descent. But there are lots of interesting unanswered questions that I either haven’t made up my mind about or have a position that is ready and waiting for new data to overturn.

Sounds good. I am pleased to know that you will no longer explicitly suggest that people here are hiding something when they don’t agree with you.

(Raymond Isbell) #196

Have you engaged with those on the other side of the argument, e.g., Mortenson, Sanford, et al. They adduce evidence and argument for the opposite view that you take. I find it valuable to get the writings of both sides and go thru them carefully to first identify where they disagree, and then analyze their arguments point by point. It usually resolves the issue quickly, but not always. Sometimes the differences are subtle, and it takes a real effort to come to a carefully reasoned position that can be defended. One of the frustrating things about trying to find the truth is that proponents of each side often engage in what I call a form of eisegesis where they begin with unverified assumptions and use them to frame the argument and then read those assumptions back into the evidence so that it sounds supportive of their view. This is classic circular reasoning/begging the question. Worse, they then extrapolate these conclusions to support other similar positions. I call it “circular eisegesis.” (False arguments supporting other false arguments until you have a whole body of untruth passed along as truth.) I find it among scientist and theologians to a very high degree. I’ve caught myself doing it, but now when I make my final pass thru my position, I look specifically to see if I’m guilty. If so, I correct and start over. It slows the process, but in the end, it’s worth it if truth is your goal even if you don’t like the outcome. What puzzles me is their refusal to admit to what they are doing, and failure to see (willful blindness?) how it undermines their conclusions. I’m seeing it on both sides of the debate on evolution vs ID vs YEC. In the SE world when you build something, the machine or system you build doesn’t understand circular reasoning, and it offers no mercy. Worse, it won’t tell you what mistake you’ve made. Reminds me of a USMC Major I worked for back in the early 1980’s. He was the proverbial hard ass. I would write a paper (any topic) and give it to him whereupon he would give it back to me with a sticky note on it saying, “There’s a typo in the paper.” That’s it. He would not tell me where the typo was located. He would add, “Welcome to the world of systems engineering where there’s no partial credit.” It was a valuable lesson both in engineering and even more so on the battlefield.

Where am I going with this little tale? Given there’s so much about the Cell that we don’t know, it seems odd that advocates of Neo-Darwinian Evolution (NDE) are so quick to conclude its truth and reject ID or YEC. There are some very intelligent and seemingly good willed persons on both sides of this debate who disagree. On the ID side, of course, there’s a long list of smart people, Meyers, Behe, Tour, Dembski, Denton, et al. On your side, there’s an even longer list. On the ID side, they seem less dogmatic as reflected in their use of abductive reasoning where they simply conclude that ID is the best explanation give what they know, but also acknowledging what they don’t know. Supporters of evolution seem much more dogmatic, and often attack any challenger ad hominem. They come across as defensive, threatened, etc. Even worse, they go out of their way to silence any challenge, especially if it hints at theism and fiat creation. I find the NDE/ID/YEC debate at the pinnacle of human reasoning and critical thinking. The process of going thru it examining both sides is a great pedagogical tool that can train one to think critically. Its use in public schools would be a sea change for the USA. Imagine a whole generation of young people coming out of school with strong critical thinking skills, and an ability and willingness to engage in respectful dialog (free speech)! Why does our education system forbid it?

Sorry for this digression, so back to my question. Have you engaged with the “other side” in a constructive manner where the real dividing issues are identified and intelligently argued and documented? If so, I would love to read it.

(Christy Hemphill) #197

I’ll let Dennis point you to his relevant articles, but I thought I’d mention Dennis was on the “other side” for a while. They are so mad that he is not anymore that Evolution News and Views dedicated a bunch of posts (I forget how many, 20?, 30?) last year to letting everyone know how terrible he is for his book Adam and the Genome. Talk about coming across as “defensive, threatened, etc.” (That also might clue you in to some of the reasons ID is not always greeted 'round these parts with warm fuzzies and terms of endearment.)

(Raymond Isbell) #198

There are zealots on both sides that add only heat, not light to the debate. It’s sad.

(Raymond Isbell) #199

I can only say, “How can you possibly understand ‘how that system got to be how it is’ without a deep understanding of its functions and systems.” A good illustration is an internal combustion engine. We know that when gasoline starts to burn it will do so slowly until it reaches a critical pressure/temperature level at which point all the gasoline will burn simultaneously (explode). Inside an internal combustion engine cylinder the spark plug ignites the fuel and the flame front grows as adjacent fuel molecules ignite the next fuel molecule. However, fuel will ignite spontaneously if it reaches a its critical pressure/temperature plus a small time delay. As the flame front progresses thru the mixture, pressure and temperature increase and reach that critical pressure/temperature. After a short time delay, the entire remaining fuel will detonate and that is know as “knocking” or “pinging.” You can hear it, but worse, it burns much hotter than normal and will burn the valves and in some cases burn a hole in the piston. Octane rating is a measure of how resistant fuel is to detonating. Octane boosters added to fuel cause the time delay to be longer so the flame front has time to burn thru the fuel before the remaining fuel detonates.

Early internal combustion engines experienced failures due to this phenomenon. Once gasoline burning was better understood and it relationship to compression ratios, fuel octane ratings and detonation was established, a new design was built that could provide the right combination of cylinder and piston size/shape and fuel with added octane boosters. Now we know how modern internal combustion engines “got to be how it is.”

I think this illustration shows that a deeper understanding of system functions can indeed show us how a system got to be how it is.

We may share a common interest since I reject presuppositional apologetics. It’s circular reasoning pure and simple. My goal is to understand science well enough that I can explain the Cell and see no contradiction with the Bible. My faith in Christ came from the Bible, not thru reason or logic. God claims there’s sufficient evidence in creation (Rom 1) to convince us to look to/accept Him as the creator and sustainer of the observed universe. He didn’t ask us to prove it. Those who accept it/take Him at His word are given eternal life because of Christ’s soteriological accomplishments. You start the Christian life as a baby (analogy) who knows virtually nothing. The phrase in Rom 10 that says “faith comes by hearing, and hearing from the Word of God…” means precisely that. No amount of human sagacity can bring you to believe. God designed it that way. (Rom 1:18ff/1Cor 1:18ff) The more of the Bible you learn, the more your faith grows. Is it magic? I used to wonder about it. I found a better explanation. The Bible is like a jigsaw puzzle. The more parts you find that you can properly place, the more the picture comes into view, and the more convinced you become that the picture on the box is correct. With over 50 yrs as a Christian and having found a large number of puzzle pieces that fit, the truth of the picture on the box has been established in my mind. As I simultaneously study science, I’m seeing fewer and fewer conflicts. My goal is to study/learn until I see the fewest conflicts possible. When I come upon a conflict, I don’t throw out the whole thing, I “put it on the shelf” until I learn more that will enable me to pull it off the shelf and place it into the puzzle.

(Dennis Venema) #200

I was the “Fellow of Biology” for BioLogos for many years, and wrote many articles about these issues over that timespan. The “Evolution Basics” series might be of interest to you because it was intended as a coherent introduction to evolution for non-specialists.

You can also find videos online of me having discussions with Young-Earth Creationists: in 2011 (I think?) I “debated” Georgia Purdom of Answers in Genesis at LeTourneau University, and more recently I interacted with Nathaniel Jeanson at a conference at Southeastern Baptist Theological Seminary.

The real dividing issue for YECs of the AiG variety is that they overtly say that no scientific evidence can change their minds. Georgia actually says this flat out in her presentation, and AiG has this as part of their statement of faith - that no evidence can ever contradict a YEC interpretation of the Bible.

(Raymond Isbell) #201

That’s unfortunate that they refuse to accept evidence they don’t understand or agree with. I think what it reflects more than anything else is that they don’t feel confident in examining and rendering verdicts on evidence on subjects they feel unqualified to judge. They’ve made a choice based on their understanding of the Bible. I can’t fault them for that, but there are some in their ranks who can formulate a better position.