Reaping the Whirlwind: protein function without stable structure


(Raymond Isbell) #282

That’s a bold claim, viz., that I profoundly misunderstand microservices architectures. Are you sure? Turns out I am aware and have worked with them and their predecessors, e.g., SOA, etc. I think I’m seeing a pattern in your thinking. You’re quick to conclude ideas are true before you have sufficient data to support it. You believe your understanding of things is so high that you can make conclusive judgments without having all the facts.

Embracing evolution is something where I’m beginning to see similar thinking. An example is to conclude that terrestrial animals are ancestors to whales. It’s possible, but is it conclusively proven or is it your best estimate based on the limited data you have? You see things like hind limb loss in dolphins that seems consistent with the hypothesis that whales are descendants of land creatures. Being consistent with is a lot different than a proof. You look at the genomics of both and conclude this also is consistent with that hypothesis. Those are good observations, and consistency says you’re going in the right direction, but a good test engineer would challenge it as proof. Just looking at the abstract of the paper that Stephen provided from PNAS on the Developmental basis for hind-limb loss in dolphins, it’s interesting to note how they see their argument not as proof but as suggestive of support for the hypothesis. Notice in the quote below from that abstract terms like “suggests,” “may account for,” and again “suggests.” That’s completely fair to recognize data as “suggestive of” or “may account for,” but not enough to conclude that their data is conclusive for the hypothesis. I see lots of this in evolutionary arguments which is fair but taking the next step to accepting it as conclusive seems unwarranted given the quantity of well-known unknowns. It seems to me that the evolutionary argument is built on the large number and consistency of arguments that are suggestive rather than conclusive.

“Interpreting our results in the context of both the cetacean fossil record and the known functions of Shh suggests that reduction of Shh expression may have occurred ≈41 million years ago and led to the loss of distal limb elements. The total loss of Shh expression may account for the further loss of hind-limb elements that occurred near the origin of the modern suborders of cetaceans ≈34 million years ago. Integration of paleontological and developmental data suggests that hind-limb size was reduced by gradually operating microevolutionary changes.” (https://www.pnas.org/content/103/22/8414.long)

It’s very similar to your belief that I “profoundly misunderstand microservices architectures.” I’m definitely not a software engineer or coder like you, but I’ve had many work for me, and I’ve guided and supervised their work. (some from BAH) My work in my last few years before retirement was closer to the sensor end of the data flow, and working with the data at its inception where it must be identified, classified, formatted, scaled, etc. In that regard, I spent the last 2 yrs working with AI strategies to exploit imagery. We’ve looked at convolutional neural nets (CNN) similar to what the Stanford Vision Lab did especially with supervised training (crowdsourcing with Amazon’s Mechanical Turk), Support Vector Machines (SVM), and others.

It’s also interesting to me that you seem so impressed with microservice architectures and that it accomplishes the simplification problem with complexity. It does that to an extent and is clearly useful, but what’s really interesting is that that strategy, simplification of complexity, is a highly abstract idea that originates with mental activity. It does not come about because of random changes to code followed by a form of natural selection. To me the very existence of microservice architectures reflects design rather than evolution. emphasized text If you randomly change the old Microsoft disk operating system (DOS) would you expect to see Windows 10 come about ever. Design is clearly the better choice. What say you?


(Raymond Isbell) #283

You clearly haven’t read the book. One of it’s strengths is its comprehensive citation of peer reviewed sources. Your response above is common among evolutionists. It’s the standard narrative rather than a reflection of an individual reviewer’s careful, critical and complete review. It reminds me of the fact that when Stephen Meyer’s book “Darwin’s Doubt” came out in 2013, a review appeared in less than 24 hrs slamming it. The book is 500 pgs and somehow the reviewer got it, read it, and wrote a scathing review all in less that 24 hrs. Would you call that honest?

I’m trying to withhold judgment on which side is correct in this debate until I’ve seen the evidence from both sides. So far what’s catching my attention the most is what the evolutionists side calls evidence. The evidence evolutionists call evidence is questionable. But I will continue to look at it since you guys seem to believe it is.


(Raymond Isbell) #284

Venema uses his (a smart human) criteria of what constitutes a good design for assessing God’s design. He then uses his conclusion that God wouldn’t do it that way as the basis for rejecting ID. That would be Ok if he could show that man’s criteria for assessing design is as good or better than God’s.


#285

I as trying to point out you are attempting use a tool created for human designs to determine how God would have designed the cell.

BTW, you are not the first and certainly won’t be the last to bring up the “man’s thoughts” argument. I was just struck by the idea that the design folks are committing the same “error”.


(Raymond Isbell) #286

Not sure I follow you with regard to denying evidence. Evidence should first be evaluated as being 1) relevant, 2) meets accepted criteria (accepted by both sides) for being valid, 3) can be logically/experimentally shown to meet the criteria.

The verse is out of context? How so? Man does not think the way God thinks in all contexts. God’s thinking is compete, 100% unbiased, righteous, and just. Show me a man who can meet that,and I’ll agree we need to limit it to some specific context.


(Randy) #287

@Raymond_Isbell Mr Isbell, I am sorry if I misunderstood. I am working in Junior Church right now but I will think and try to get back to you later today. Thanks.


(T J Runyon) #288

Nick was spot on though. You still haven’t answered my question about the origin of Homo. Evidence for what? I’m 99 percent sure you and the book’s author have no idea what he means.


(Raymond Isbell) #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:

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?


(T J Runyon) #290

What would show this for you?


(Raymond Isbell) #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.


(Stephen Matheson) #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):


#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.


(Jay Johnson) #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.


(James McKay) #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?


(Raymond Isbell) #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.


(Raymond Isbell) #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.


(Raymond Isbell) #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.


(James McKay) #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.


(Stephen Matheson) #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.


(James McKay) #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.”