Reaping the Whirlwind: protein function without stable structure

Faith & Science Conversation
289

I disagree. I’m using SE to try to determine how God designed the cell. The results will inform my effort to decide if evolution is the best explanation or design. Remember, we would choose design if it appears that it most likely comes from mental activity. We would choose evolution if we had compelling evidence that the Neo-Darwinian process can produce the result. So far I’m seeing weakness in the evidence offered by evolutionists. I’ve suggested recently that the evidence offered by Venema in his video is not scientific evidence. At best the kind of evidence he offers is consistent with the evolutionary hypothesis, but consistency is not proof. Also, it seems that if you see many evidences of this ilk then you claim that it raises the quality of the evidence body to a level where it can be declared proven. Similar to this approach is the appeal that 90% or more of scientists believe in evolution.

I asked earlier in this forum for a single piece of evidence that shows macro evolution has been proven. I was pointed to bacteria which is a demonstration of micro evolution, and the cetacean ancestry line of evidence. The latter is where we are now. It shows nothing conclusive, but lots of “consistent with” type of evidence. It’s useful, but it won’t get the ball across the goal line.

Show me something where we can agree 1) it’s relevant, 2) meets jointly accepted criteria, 3) can be logically/experimentally shown to meet the criteria.

Regarding testing, I notice the following test he proposed:

Upload
Upload1280×718 112 KB

If I recall, a scientific hypothesis must make a prediction that can be tested. A valid test must be 1) relevant, 2) have criteria for success that is universally accepted by all scientists, 3) via logic/experiment show the test outcome meets the criteria for success. In SE circles a V&V (validation & verification) action must be performed to show the test is a correct test (validation) and that it met the success criteria (verification).

Looking at Venema’s example, I first note that it’s a good and fair hypothesis. The prediction part of it is not so good. First, the subject is the “fossil record” and the prediction is that it has been preserved. The fossil record is not complete and therefore has not been preserved, and there’s good reason to believe it will never achieve a level of continuity that will enable a reliable test. The prediction sets as a criteria a “blurring of the distinction” between four-limbed, land dwelling mammals and modern whales. “Blurring the distinction” between two objects must have some scientifically measurable and universally accepted detail. He offers none. I suppose that he’s assuming the measuring instrument is the human visual system which includes an optical sensor, a communications network, an image processor, and finally a deep learning neural net where all the neuron weights and bias have been set and calibrated to a known standard. Finally, the test and its results must pass the V&V evaluation.

Does Venema’s Hypothesis/Prediction/Test measure up?

Thoughts?

290

What would show this for you?

291

An example where a hypothesis is made and an associated prediction that has a test outcome that is unequivocal and meets the standards for testing I outlined above. If evolution is true and considered fact by most of you, then there should be plenty of examples. I just haven’t seen one yet.

292

It would be so interesting to discuss this conceptual interface between biological systems and modern computer science. Yesterday I was reading a review article on cryptic genetic variation (CGV), and the conceptual basis of that field is (largely) Waddington and his theory of what we have been calling robustness. (Side note: it’s strange to see how this thread, tedious and frustrating though it is, is paralleling real scientific conversations and research in my professional sphere.) A major point of the article is that cryptic genetic variation (defined as genetic variation that does not reveal itself in the detectable characteristics of the organism), first revealed in Waddington’s experiments and validated brilliantly since, is a major source of evolutionary raw material.

But here’s my question for you. CGV is not mysterious; it’s just a form of genetic variation. What makes it interesting is the fact that it is “conditional-effect genetic variation.” Its influence is only seen under particular conditions, and one of the big research questions is about how it is established and maintained. This sounds just a bit to me like an “event-driven system.” In particular, I am intrigued by this sentence in the blog post you quoted: “An event-driven system where something isn’t quite right is more likely to do most things well, some things OK, and a few things poorly.” I’m not formulating my question very clearly, so maybe I’ll just leave it with you to see what happens. :smile:

Here is the article on CGV if you want to have a look (PDF of final version at the journal available on request from me):

2 Likes
293

A human tool to determine how God designed the cell. You don’t see the problem with this?

Mental activity of a human sure. So now you are saying you can know the mind of God. Didn’t you just quote a Bible verse that says basically we can never know the mind of God?

The prediction is not that a total and complete fossil record would be found. Just that the fossil record shows the transition from land dwelling mammals to modern whales. Does the fossil record show, for example, that the appearance of first aquatic mammal is later than the first land dwelling mammal? Did the first aquatic mammals still have 4 limbs? Etc, etc.

That will never happen, which is when you fall back on the consensus position. Being aware that what is accepted by 98% of scientists today may not be in the future. But that is the way the science cookie crumbles.

2 Likes
294

You don’t understand how publishers operate. Review copies are sent out well in advance of publication for “major” or important books. I would call it “Standard Operating Procedure.” Go have a look at this thread:

Seems that there’s a review of Behe’s new book in Science magazine, even though the book isn’t for sale yet. Despite the fact that you have no experience or knowledge of the publishing industry, you are bold enough to insinuate that the 2013 review of Meyer’s book was dishonest, since the reviewers couldn’t possibly have had time to read the book. This is the same dubious procedure you are using in your “evaluation” of evolution.

I don’t need to read “Contested Bones,” because I read the authors’ own article describing the book, and because I have spent the past two years researching the same “peer-reviewed sources” that they reputedly surveyed. The authors’ conclusions are ridiculous, and I can definitively say that they either are incompetent readers or else they willingly misrepresented their sources. If you want to actually learn something about evolution, you need to leave off reading propaganda and start reading actual science. Only then will you be able to sort the wheat from the chaff on the subject.

2 Likes
295

Hi Raymond,

I don’t think Chris is making unsubstantiated assertions when he says you misunderstand microservices architectures. He’s basing this assertion on the fact that you’re making claims about them that are simply incorrect.

This is understandable mind you. It’s very, very common for people with extensive experience in IT to believe that they’re working with microservices, Continuous Delivery, DevOps, Agile and the like when they’re doing nothing of the sort. This is especially the case if you’ve worked mainly in organisations where they try to introduce these practices into a culture that is heavily steeped in more traditional “best practices” such as change management. Some of the misunderstandings of these concepts that I’ve encountered in my career have been seriously screwy.

To be honest, if you want to claim that you understand microservices, DevOps, Continuous Delivery and the like, you really need to have steeped yourself in that particular culture and worked and interacted with people who are pushing the envelope as hard as they can with these technologies.

Do you have any experience with Kubernetes?

2 Likes
296

Yes, it’s called science. Oscilloscopes, microscopes, micrometers, RF antennas, etc. God gave us minds to build and use them. Sort of like he gave us our minds to build a wheel, pulleys, and (don’t be offended) to recognize design when we see it. SE is one those mental organization, classification, and analysis tools that he expects us to use to live productive lives. If I’m wrong, please correct me.

I can see you’re trying to catch me contradicting myself. Would that be evidence for evolution? If so, what would the hypothesis, prediction, and test be? Kidding aside, the answer is that we can know the mind of God. It’s the Bible (1 Cor 2:16). Isa 55 means that man in his fallen state cannot think like God or do the things God would do. (Adam can confirm that.) God must reveal Himself to us. Man has to learn it…usually the hard way.

You’re leaving out some important details. By “show” do you mean “proves” or “is consistent with?” If the former, I need to make a public declaration. If the latter, there’s still work to do. And remember, two or more “is consistent with” is not equivalent to “proves.” (at least in the engineering world)

Agree, but it would be interesting to see what the error budget looks like on a consensus model.

297

All of them? No exceptions?

Interesting observation. Sounds like you embrace the idea that “is consistent with” carries more authority than “proves?” Is that true? If you’re correct, then please help me to adjust the way I would assess the Hypothesis, Prediction, and Test strategy. How many “is consistent with” would it take to be equivalent to one “proves?”

You may think I’m toying with you, but those are serious questions. I think the key to understanding evolution as you and the others in this group do is to see how you view evidence, and what thresholds evidence must meet in order to be considered conclusive with virtually no chance of being wrong.

298

Are you sure I haven’t?

Recall that I pointed you to guys the INCOSE Complex Systems Working Group. You really should look at the Primer (https://www.incose.org/docs/default-source/default-document-library/complexity-primer-overview.pdf?sfvrsn=91dd81c6_0)

To show you some of the scope that will motivate you to look at it, here’s a quote from slide 9 of their PP presentation:

Concepts that seem essential:

  • Emergence: Features/behavior associated with the holistic system
    that are more than aggregations of component properties

  • Multi-scale behavior: System not describable by a single rule,
    structure exists on many scales, characteristics are not reducible to
    only one level of description

  • A system with self-organization, analogous to natural systems, that
    grows without explicit control, and is driven by multiple locally
    operating, socio-technical processes, usually involving adaptation

At least browse thru the Primer. Then you can challenge my experience level. You might be surprised and begin to see why I’m stressing SE for understanding the Cell.

By the way (and this is probably more for Stephen) the Primer might give you some ideas for research, and give you some criteria for evaluating research proposals.

299

Raymond, let’s just say that what you are saying about microservices, DevOps, Continuous Delivery and so on are completely different to (a) what I was working with for two years on the DevOps team for the new website at the Houses of Parliament, or (b) what I was learning about at conferences such as the AWS Summit, Container Camp and the like in London. On the other hand, it has a lot more in common with the “old guard” who were into Change Management and ITBM, who freaked out at the thought of deploying to production several times a day, and who had no understanding of the concept of canary deployments.

I’m not doubting that your experience of systems engineering in general is extensive. But what I am doubting is that your experience of microservices architecture and DevOps in particular is up to date with the latest cutting-edge practices. That’s why I asked you in particular if you have any experience with Kubernetes.

INCOSE looks interesting (though, as I said, somewhat architecture astronaut-y), but in more than a decade of enterprise software development, I’ve never heard anyone even mention it. I may take a look at it at some stage if time permits.

2 Likes
300

The primer that Raymond links to is interesting. Its main purpose is to unpack the word/concept ‘complexity,’ and that’s pretty helpful and interesting. In recent meetings with some evolutionary biologists, I heard leading scientists complaining about ambiguity surrounding the term, for reasons that sound the same as the ones mentioned by the working group. Beyond that, the primer is a list of things to think about and a lot of different directions one could go in thinking or designing, and that does seem less useful to me. (I can’t speak for astronauts.)

I don’t know why anyone would think that the primer points toward research ideas in evolutionary biology, but maybe that’s because I think evolutionary systems biology already knows the various concepts that are listed in the primer. More interestingly, I see that the working group seems explicit about the converse: getting SE to learn from–and to adopt the ‘tools’ of–evolution. Namely variation and selection. That’s not new, at least not to scientists, who have created a subdiscipline for the use and study of evolutionary processes in design (of, for example, chemical inhibitors with drug potential).

Now I’ll go back to spectating as you and @Chris_Falter give a clinic on computer science.

1 Like
301

A lot of thinking in modern software/systems engineering is influenced by ideas from biological evolution these days. Enterprise architects are now increasingly talking about concepts such as architectural fitness functions, for example.

This thread has given me an amusing reminder of my last experience with formal tuition in biology, when I was at school as a teenager. We were given, as a homework exercise, the task of writing about the differences between instinct and learned behaviour. I wrote one paragraph about how instinct was like read-only memory and how learned behaviour was like random access memory, then went on to write a page and a half about computer architecture.

My biology teacher described it as “some interesting points of view.”

3 Likes
302

One of the quotes he provided from the book from a paper by Wood is from the first paragraph of the paper. He and the author totally ignore the rest of the paper.

1 Like
303

My point is God wouldn’t use any of the instruments you mention. So why would how God chose to design a cell be visible to those limited human instruments. You basic assumption is God designs just like humans design. Thinking I guess that God is just as limited as humans. While that may be true for your conception of how God works it isn’t for me. I am not trying to prove evolution. I am just asking why you think your conception of design is exactly like God’s. For instance, my God could design a cell without using C4 or other acronym of your choice. This would make His design invisible to you wouldn’t it?

Where is the chapter on cell design again? I must have missed it. The Bible tells us that just contemplating the nature we can see with our naked eye is all we need to see the God.

And yet here you are trying to think like God and deciding how God would do something.

When you get up to the thousands is that good enough for you? Remember people have been trying to disprove evolution from the beginning and it hasn’t happened yet. But I guess since you still have your doubts that in itself makes it not good enough.

304

Of course, once you get the quote you want you stop digging, I mean you stop reading.

1 Like
305

Makes for good eisegesis, though!

306

This is a long thread, and I don’t have the time right now to get much context for this reply. But I will respond to @DennisVenema’s queries.

Virtually all modern cetaceans have small pelvic bones in the body wall that develop as a part of the hind limb bud early in development. Generally speaking, these cetaceans only have the two very simplified pelvic bones (one on each side) in the body wall. However, there have been a number of rare documented cases in which external hind appendages developed (see Ohsumi and Kato, 2008, A bottlenose dolphin (Tursiops truncatus) with fin-shaped hind appendages, Marine Mammal Science 24: 743-745.) or additional bony elements developed in sequence beyond the pelvic bones (including a very rudimentary femur, tibia, tarsal, and metatarsal in a humpback whale; see Andrews, 1921, A remarkable case of external hind limbs in a humpback whale, American Museum Novitates 9: 1-6). I don’t know too much about the molecular and developmental mechanisms behind this (@sfmatheson notes a good paper about this), but I do know that we can document the morphological changes in Eocene protocetids and basilosaurids as cetaceans went from semiaquatic to fully and obligatorily aquatic. In basilosaurids, we still have all of the bony elements of the hind limbs (from pelvic bones down to toes), though these appendages are far too small for weight-bearing. (I’ll also correct Dennis here: the astragalus in Basilosaurus is not recognizable as a double-pulley astragalus because it is fused to several other tarsal bones. However, the astragali of all earlier archaeocetes match the basic morphology of artiodactyl astragali.)

I’ll also echo the fact that there are tons of independent lines of evidence for cetaceans’ terrestrial ancestry that span multiple fields. I’ve given a number of lectures that speak to this, some of which are available online if you’re looking to listen.

5 Likes
307

Hi Raymond,

Let me say how tremendous respect I have for good program managers. They have to excel in a variety of disparate tasks:

  • Understand and conform to regulations and contracts.
  • Understand the objectives of a system, and make sure the accepted proposal meets the objectives.
  • Understand the regulatory and legal environment, organizational capabilities, and technology stack well enough to be able to identify constraints, dependencies, and risks that need to be managed.
  • Work with stakeholders to make sure constraints, dependencies, and risks do not derail the project.
  • Understand systems development methodologies well enough to make sure the stakeholders are working together successfully toward milestones.
  • Be able to identify the voices in the cacophony that need to be paid attention to, and to tune out the rest.
  • Fly faster than a speeding bullet, leap tall buildings in a single bound. :smile:

I am sure you could add a lot more that I missed, Raymond.

However, an excellent program manager who has “worked with” a technology stack can be very successful despite having a very superficial understanding of the technology. This is not due to lack of education, capability, or intelligence; it is the inevitable result of having to spend so much time and effort managing.

In spite of my affection for good program managers such as you, Raymond, I cannot say that your professional experience makes you qualified to understand any particular technology at the level of depth required to evaluate its suitability as an analogy for biological processes. If you want to demonstrate sufficient expertise, you need to make accurate statements about the technology.

You made inaccurate assertions about microservices. Those inaccurate assertions demonstrated a profound lack of understanding about microservices. Ultimately, it had nothing to do with your professional experience.

I mentioned your professional experience solely because you yourself had made a big deal about your SE experience. The only way I could imagine to reconcile your self-presentation of your experience, on the one hand, and your inaccurate statements, on the other, was to assume that your experience was in areas other than the ones in which you made inaccurate statements.

I made the conclusion about your microservice expertise based on your erroneous assertions about the subject.

Your statements were the facts I relied upon.

You mention computer vision algorithms without realizing how little they help you understand the subject I spoke of, viz., deep reinforcement learning. Here’s why: deep reinforcement learning is part of a completely different family of machine learning algorithms than the family that includes computer vision.

In a nutshell, machine learning has 3 different family of algorithms: unsupervised (e.g., k-means clustering), supervised (e.g., convolutional neural networks), and reinforcement learning (e.g., self-driving vehicles). Understanding one family of algorithms does not imply that you understand the other two.

Serendipitously, it so happens that the mathematics of CNNs provide a pretty good analogy for understanding how biological equilibria develop. Are you interested in discussing that topic? If so, I can share more thoughts.

Publishers often distribute pre-publication copies to reviewers. Sometimes reviewers share them with friends, acquaintances, or other interested parties. Therefore there is no reason to question anyone’s honesty in this situation.

My daughter is a book publicist; she managed the book tour for Chris Christie’s “Let Me Finish.” The Guardian (U.K.) published a review of the book 14 days before its publication date. Nevertheless, every statement they made about Christie’s book was accurate.

Sure, it’s not a perfect analogy. The reason I mentioned microservices is that you insisted that SE principles for monolithic architectures proved that highly complex systems require the extremely careful orchestration of dozens of changes. Microservices are relevant because they demonstrate that the SE principles that were so prominent in your thinking do not apply to all complex systems. And if they are not applicable to microservice-based systems, perhaps they are not applicable to biological systems either.

Microservices are not the only technologies I have mentioned. I have also proposed deep reinforcement learning and evolutionary algorithms (IIRC) as better analogies to biological systems.

I agree 100% with you that God designed the universe and life for His purposes, and it is only by His continued providential interaction with us that we subsist.

I do not think that we can arrive at this faith conclusion on the basis of the scientific method or of SE principles, however. I am convinced that such faith is a gift that comes through the revelation of Jesus Christ.

Have a good and blessed week, Raymond.

3 Likes
308

My daughter works in the industry, and she tells me that this is how all publishers (other than vanity presses) operate.

Would you agree with me, Raymond, that the burden of proof should rest on the party that asserts an exception?

1 Like