Reaping the Whirlwind: protein function without stable structure

(Raymond Isbell) #262

Since most of the readers in this group won’t read this book, I’ll provide the review on Amazon that I provided last year. Here’s my review:

Contested Bones is an excellent book. Its content is expertly designed and written, carefully argued, and well supported by the scientific literature. The book demonstrates that the ape-to-man hypothesis is far from compelling. Citing a wide range of sources from the scientific literature (e.g., Nature, New Scientist, Scientific American, etc.) the authors have demonstrated that there is a serious lack of consensus within the scientific community on the ape-to-man story-line. Chapter 2 is titled “A Theory in Crisis.” It cites Bernard Wood, a paleoanthropologist from George Washington University where he says, “Even with all the fossil evidence and analytical techniques from the past 50 years, a convincing hypothesis for the origin of Homo remains elusive.” (Nature 508:31-33, 2014) The bulk of the book critically examines details of various fossil finds (e.g., Homo neanderthalensis, Homo erectus, Homo floresiensis, Australopithecus afarensis, Ardipithecus ramidus, Homo habilis, Australopithecus sediba and Homo naledi.) and shows that there is wide disagreement on their classification within the paleoanthropology community. Of particular interest to me was the Chapter on Dating Methods. Evolution requires time for the Neo-Darwinian mechanism to work. Can the earth be shown to be 4.5 billion years old? Rupe examines carefully the argument behind the most popular dating techniques (e.g., potassium-argon, argon-argon, Uranium-Thorium, and Uranium-Lead.) The depth and clarity of this chapter convinced me that the dating methods are not reliable. Rupe’s analysis is impressive and critics will strain to find fault. He supports his case with many citations from the scientific literature. This is the only book I’ve found that treats the subject with sufficient rigor to be convincing. The final topic of the book addresses the genetic evidence. Written by John Sanford, a true expert in the field, this chapter is quite revealing. Sanford has noted something that I personally have found true as I’ve investigated the evolution-creationism debate. Sanford notes, “It is true that most scientist are committed to the evolutionary framework, yet it is surprising that this strong commitment is not usually based upon the scientist’s own person experience or expertise. Most scientist need to look to experts in other fields (or even the popular media), to find support for their certainty about human evolution. This can become circular-scientists are consistently looking to other scientists to justify their personal certainty about human evolution.” Sanford concludes his introduction to this Chapter (13) by saying “Contrary to popular opinion, the genetic evidence does not support ape-to-man evolution. In fact, it strongly refutes it.” (pg. 286)
In summary, Contested Bones, is a valuable contribution to the literature arguing against the ape-to-man hypothesis. It’s well written, professional, and technically competent. It’s a must read for anyone with an interest in the ape-to-man evolutionary hypothesis and is an excellent reference source to what the scientific community is really saying, and not what the media is reporting

(Raymond Isbell) #263

I’ll take a look. Thanks.

Gosh, only 47. Are you potty trained yet? At 72, I’m entering the home stretch, and enjoying it immensely. By the way, I give the ID and YEC folks a hard time too. Sadly, it’s hard to find Christians today who can give a good accounting of what they believe and why. The words of Amos may be applicable to our day:

Behold, the days are coming,” says the Lord GOD,
“That I will send a famine on the land,
Not a famine of bread,
Nor a thirst for water,
But of hearing the words of the LORD.
12They shall wander from sea to sea,
And from north to east;
They shall run to and fro, seeking the word of the LORD,
But shall not find it.

The New King James Version. (1982). (Am 8:11–12). Nashville: Thomas Nelson.

(Randy) #264

I think I appreciate an undercurrent of what you are saying here…let’s focus on what is important. In 1 Cor 13 we read, "If I… can fathom all mysteries and all knowledge, …but do not have love, I am nothing.

4 Love is patient, love is kind. It does not envy, it does not boast, it is not proud.5 It does not dishonor others, it is not self-seeking, it is not easily angered, it keeps no record of wrongs. 6 Love does not delight in evil but rejoices with the truth. 7 It always protects, always trusts, always hopes, always perseveres.

When I was a child, I talked like a child, I thought like a child, I reasoned like a child. When I became a man, I put the ways of childhood behind me. 12 For now we see only a reflection as in a mirror; then we shall see face to face.Now I know in part; then I shall know fully, even as I am fully known.

13 And now these three remain: faith, hope and love. But the greatest of these is love.

As I grow older, I realize that without the important things…love of family, God, justice, mercy…even knowledge is nothing. And trusting God has truth and justice at heart reminds us that even if we don’t fully grasp everything, it doesn’t really matter so much on the grand scheme of things. I appreciate your interaction.

(Chris Falter) #265

I understand it quite well.

You reject the fact that a complex, integrated, system-of-systems microservice architecture with devops pipeline does not, by and large, suffer from the problems that plague the kinds of systems architecture you have experience with. You have not yet reckoned with the fact that every day of the week Netflix proves you wrong hundreds of times, and Amazon proves you wrong literally thousands of times.

So allow me to ask you: Have you ever been the program manager for a big microservices based system that uses a well-lubricated devops pipeline? (And no, I’m not talking about a system that tries to switch over, big bag, to m-services without a proper ramp-up.)

Of course I cannot blame you for lack of personal experience. However, let’s take a look at your allegation that folks are not paying attention to your SE arguments. Try to step outside your own emotions for a moment and consider this: What might someone else say about how you have taken into account–or not–the Netflix and Amazon evidence?

I would also like to point out that deep reinforcement learning projects like AlphaGo and Waymo have evolved command-and-control capabilities that an army of programmers writing thousands of interacting C++ or Java modules could never hope to achieve. This is a big subject, of course. While you have studied it at least a little, I am not sure that you have kept up with the remarkable advances in the past 2 years.

As long as you insist on perceiving every issue through the grid of your own professional experience, you can be quite sure you will never understand why biologists have come to the conclusions they hold. Whether that is a problem or not is a question you will need to answer for yourself.

Have a good weekend,
Chris Falter

(Chris Falter) #266

I would like to provide some feedback to you for your consideration, Raymond.

I did the article carefully, and I’m wondering whether we read the same article.

Here, for example, is another quote from the article:

In order to study genetics, however, we don’t need to consider objects as tiny as subatomic particles. Rather, the spectrum of integrative levels that ranges from macromolecules to populations is most relevant.

And another:

Based on our knowledge of macromolecules, we would not have been able to predict that they could combine to form a living organism

It is possible that you are right and Ingrid Lobo, Ph.D. is just wrong about genetics. However, it is not possible, in my careful reading of your forum posts and her article, that the two of you are in tacit agreement.

(Dennis Venema) #267

The “bone anchor hypothesis” sounds to me like Raymond has confused leg bones with pelvic bones. There are (greatly reduced) and disarticulated pelvic bones in adult cetaceans (whales, dolphins, porpoises) and they do indeed provide muscle attachment points.

When it comes to hindlimbs, though, none of the structures persist into the adult form. No limbs, no bones, no nothing. So why start making them in the first place? So no, the “muscle attachment hypothesis” doesn’t work here.

Of course, the evidence for the terrestrial ancestry of cetaceans is not just hindlimb buds. There are scores of shared derived characteristics that are morphological in nature, and the real deal-sealer is of course the genomics. All of the lines of evidence point in the same direction.

Edit it seems like there might be some small leg bone remnants in modern whales. This isn’t my area of expertise. They look pretty small and I’m doubtful they would have much in the way of muscle attachment points, but I could be wrong. The real expert to ask would be @RyanBebej , who actually studies ancient and modern whales.

Keep in mind that we see a progression of hindlimb loss in the fossil record - the Basilosaurids, for example, have tiny hindlimbs that could not have possibly supported their bulkly, water-adapted bodies. These hindlimbs have the characteristic astragalus of artiodactyls even though this is a fully aquatic organism. So the presence of some leg bones in modern whales is not out of the question.

That said, there’s no reason to form an external hindlimb bud if all you need to do is form some internal bones in a certain spot. Why the external bud?

(T J Runyon) #268

What do you think he means here?

(Raymond Isbell) #269

My apologies. I should have said, “Just read the sentence rather than the full article.” Notice that sentence, “Thus, our understanding of physical and chemical properties in lower levels of organization helps us understand only SOME of the properties of living organisms, which prevents (or “limits” since the lower level understanding helps SOME) use of a reductionist approach.” If understanding the lower levels helps SOME, wouldn’t it be better to say that the reductionist approach has limited value? If I were the author, I would have used “limits.” “Prevents” is a little too sweeping. (Like saying “never.”)

Also, I think you missed where she established her context in the 2nd paragraph of the article which you quoted to me above. She says, “In order to study genetics, however, we don’t need to consider objects as tiny as subatomic particles. Rather, the spectrum of integrative levels that ranges from MACRO-MOLECULES TO POPULATIONS IS MOST RELEVANT (Figure 1).” She’s specifically stating that a range of integrative levels are relevant. If lower levels in that range are not useful, it’s odd that she would declare them to be relevant.

Also, I do take exception to this statement at the end of the 3rd paragraph under the section titled “Emergent Properties,” viz., “Likewise, our understanding of the new emergent properties at a higher level DOES NOT HELP US UNDERSTAND THE PROPERTIES OF THE LOWER LEVELS, because each integrative level of organization has its own particular structure and emergent properties.” An example of a system where understanding the higher levels informs the lower would be in building a large ship where wave action and bending forces on the ship establishes how strong I need to make the rivets and welds of the component parts of the ship. Information flows in both directions and is critical to understanding the full design.

From this post and your next one, I sense that you are more focused on discrediting me rather than my argument. We clearly have different experience levels. I had to have a deep understanding of metal oxide semiconductor physics and the parasitic effects across the Gate, Source and Drain junctions to establish operating ranges of voltage and current to ensure they could operate in a larger power distribution system context. Turning physics into data is a critical step that data scientist don’t normally get into. It wasn’t just data that I had to deal with, but lower level physics, and a variety of systems on up to the data management portions. Have you worked with RDF triples? it’s a great way to capture physical data attributes and put them into a format that will allow analysts to reduce the data to information helpful at the higher levels. It sounds like your experience level is only at the data end of systems. You cite Amazon and Netflix as examples of complex systems that have conquered the complexity problem. The Cell is closer to the kind of problems I have worked on since it involves not just the data (DNA) and genes, but also the lower levels where the physics of the molecular interaction and the data to represent it are at play. If the model you have in your mind for the cell is that of a simple ordering/transportation/distribution/accounting system like Amazon, then it may be understandable why you so easily embrace macro-evolution. We live in a much more complex world than data science.

(Raymond Isbell) #270

This stresses a point I have been trying to make since the beginning. If your “evidence” is not conclusive to prove your hypothesis, keep the doors open for new information. The Hippo to Whale narrative strikes me as “not conclusive.” There’s nothing wrong with withholding judgment until you have a stronger case. To me evolution has some serious limitations that should give a good scientist pause. My door is still open. I want to understand better the thinking behind evolution.

Back to your question, I think he means that the evidence is not conclusive. So adding an argument that we know the origin of Homo to support evolution is premature. He’s qualified and says we need more substantial evidence. I’m seeing the same thing. Evolution’s scientific support is weak. Its strength comes from biological eisegesis and heavy extrapolation. If you read in the ID and Creationist literature, you’ll see that there are some credible alternative explanations for some of this evidence. Read both sides of the argument. Don’t decide which is right first, then search for evidence. That’s a recipe for a bad outcome.

(Raymond Isbell) #271

This is an example of the kind of argument that interprets evidence in an invalid way. Is man’s view of how it should be done the criteria for determining truth? I’ve seen this argument pushed by some famous atheists like Dawkins, et al. “It’s not a good design by human standards, so it proves that ID is not the cause.” Really?

Here’s another similar type argument. It’s an appeal to what man thinks is reasonable. Isa 55:8-9 says:

8“For My thoughts are not your thoughts,
Nor are your ways My ways,” says the LORD.
9“For as the heavens are higher than the earth,
So are My ways higher than your ways,
And My thoughts than your thoughts.

We should be careful about using our sense of what is best and what is not in this world.

The New King James Version. (1982). (Is 55:8–9). Nashville: Thomas Nelson.

(Stephen Matheson) #272

The loss of hindlimbs in cetaceans (dolphins and whales), and separately in snakes and legless lizards, has an interesting developmental explanation. One reasonable hypothesis could have been Hox gene-related. (Hox genes are famous for directing developmental patterns by–simplifying a bit here–directing a particular sector of the body to turn into a particular kind of anatomical structure.) That hypothesis would predict that changes in Hox gene sequences or expression patterns would result in the hindlimb never forming. Another less-specific explanation would involve inactivation of one of the key genes in limb formation.

Developmental biologist showed that hindlimb loss in the two overall lineages (whales and snakes) is different. In snakes, the Hox gene mechanism largely explains limblessness. But in whales, the key change seems to be loss of signals that cause distal limb development. (Distal = outer, so the distal limb is forearm and hand in humans). So, the outer hindlimb structures start to grow then degenerate, leaving the smaller limb bud behind. A 2006 paper (below) described the underlying genetic mechanism. As far as I know, no one has comprehensively looked for the mutations or other genetic changes that drive this.

(Chris Falter) #273

Okay, I can go with this formulation now that you’ve explained it. Thanks for delving into the details with me.

At the same time, you have now no doubt come to the realization that reasoning from the lower levels of SE principles can only offer limited insight into what’s happening in the higher strata of biological systems. Not all properties at the biological system are emergent, so yes, SE can help us understand those non-emergent properties. But what about the numerous emergent properties of biological systems? SE principles cannot help us understand them.

What biologists have been telling you, Raymond, is that the evolutionary origin of biological systems is one of those emergent properties that SE does not help you understand.

I have as much experience with RDF triples as you have with micro-services architectures and devops pipelines, I suspect.

You profoundly misunderstand microservices architectures, my friend Raymond. Lower level interactions–the physics of molecular interaction, to borrow your analogy–are very much dealt with in a micro-services system of systems. The key insights you are missing are:

  • The “molecular” interactions are encapsulated within the boundaries of a micro-service
  • Those micro-services are loosely coupled via a messaging infrastructure
  • Long-running processes use the saga pattern to perform work
  • Event-driven interactions are fundamental to the work, and often yield emergent behaviors.

The systems built on micro-services architecture are actually much more similar to biological systems than the procedural-style and object-oriented systems I spent most of my career working on.

I don’t necessarily expect someone who has not worked on m-services systems and systems of systems to grasp this out of the gate. But I would hope that someone who has no professional experience with these kind of systems would recognize the limitations of their understanding, rather than making unwarranted assumptions about them.

Edit: Amazon built the AWS platform to facilitate their own systems of systems, then made their capabilities public so others could for a price use the same architecture. I phrased my argument in terms of AWS, but of course it applies specifically to Amazon’s own systems.

You profoundly misunderstand AWS architecture, my friend Raymond. Profoundly.

AWS architecture very much involves the concerns of electrons and transistors and logic gates, etc.

It’s just that these kinds of physics concerns are encapsulated at a lower level of abstraction. The encapsulation is successful enough that admins, architects, and developers who build m-service systems and systems of systems on AWS don’t need to worry about them; they spend their time thinking at higher levels of abstraction.

100.00% incorrect. Over the course of my career I have written hundreds of KLOCs in at least 8 different languages. Here is my LinkedIn profile so you do not need to make assumptions about my professional background. :slight_smile:

You are expressing no curiosity about how deep reinforcement learning has evolved command-and-control logical systems layered on top of physical controls. This has been a very fast-moving field in the past 2 years, and it provides obvious analogies to biological systems.

And BTW, a deep reinforcement learning system does involve physics concerns. Practitioners work hard on setting the hyperparameters of the systems in such a way as to maximize the learning rate, given the physics constraints involved.

Have a good weekend, Raymond.

(Jay Johnson) #274

I highlighted the last bit because I’m glad to hear it. You’ve been reading propaganda written by apologists, not science written by scientists.

In Rupe and Sanford’s own words:

We have spent four years carefully examining the scientific literature on this subject. We have discovered that within this field (paleoanthropology), virtually all the famous hominin types have either been discredited or are still being hotly contested.

I have spent the last two years carefully examining the scientific literature on this subject, and I can definitively say that Rupe and Sanford twist the truth to fit their narrative. Go back and watch the video series that @Bill_II linked for you. Go read Joel Duff’s blog that I linked for you.

Rupe and Sanford resort to a tried-and-true tactic of the YEC apologist, which is to highlight specific debates within a scientific discipline, then blow up these proper and normal scientific discussions into a THEORY IN CRISIS! (A little like the caravans headed toward our southern border, but that’s neither here nor there.)

Honestly, one of the most disappointing things about my own journey has been the discovery that many Christian apologists have no problem with lies and distortion, as long as they are “defending the truth” of the gospel. I’ve removed many books from my shelves in the past few years.

Getting back to the point, when your whole case against evolution is built on one or two “experts” out of a hundred who disagree with the consensus (and there really is a consensus) on a single point of fact, start multiplying that .02 by the number of various points of fact and lines of evidence that one must disagree with in order to maintain the position that evolution could not have occurred. As all these exceptions to the consensus continue to multiply, the chance that all of them are true starts to become vanishingly small (.02 x .02 x .02 x .02 … etc.). It seems the ID strategy of calculating the improbability of evolution turns back upon itself in the end. How many “what ifs” and “maybes” can a proposition hold before the straw finally breaks the camel’s back?


So man’s view of design (you did point out the studies that show how good humans are at seeing man made design) is now the criteria for determining how God would design? How do you know that God would design something in the same way as a human?

“If it is a good design by man’s standards that proves ID is the cause”

(Stephen Matheson) #276

For me and others I know, the persistent failure of Christian faith to make a difference in the minds of believers, to stimulate and reinforce integrity, is such a dramatic weakness that it justifies rejecting Christianity. This very thread has provided me with something I don’t want to get from the forum: a reminder of why I left.

(Jay Johnson) #277

Sorry for inadvertently opening old wounds. I see a lot of persistent failure when I look around the Christian landscape these days, but I’ll spare you my apologetic. Sounds like you’ve had enough for one day.

(T J Runyon) #278

Evidence for what?

(Stephen Matheson) #279

Aw, you’re the best, but no worries, I just meant that I don’t come to BL to be down on Christianity. And I can get reminders of why I left hourly from the news.

(Randy) #280

Care, yes. Always. Deny my eyes’ evidence? No. How can we talk with anyone by saying presuppositionally that we are correct? This unfortunately does not work. And the verse is out of context. Thanks.

(Chris Falter) #281

Hi Raymond,

I recently mentioned the importance of event-driven interactions in a microservices architecture. Phil Windley has written an interesting post that explains this in greater detail:

Creating event-driven systems that respond in a certain way is a talent more akin to throwing a really good party, than that of directing a play. You have less control over what happens at the party, but you also have less chance of things going completely off the rails and crashing or falling flat. 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. A request-response system where something isn’t quite right is more likely to just not work at all. Event-driven systems are more resilient. Their failures are more linear–that is, small mistakes are likely to result in small, not large, failures.

If I am not mistaken, Raymond, your experience is focused on architectures with deterministic interaction patterns (such as request-response). Windley agrees with you (as do I) that these kinds of deterministic inter-system interactions are very fragile and require the kinds of extremely careful, top-down SE practices you have described at length.

However, as Windley points out, the resilience of event-driven interactions within microservice architectures makes them vastly more tolerant of errors than the kinds of architectures that you seem to have worked with professionally.

Event-driven interactions within biological systems (think gene regulatory networks, hormone messaging, neural messaging, immune response, etc.) look to have a “style” that is quite close to event-driven, microservice architectures. And they are quite far from the top-down designed, deterministic interaction, “physics-based” systems you mastered in your career.

It is wonderful that you had the opportunity to serve our Lord and serve our world by leading system-of-systems projects to successful outcomes. That is truly to be commended. Your experience gave you a wonderful tool–systems engineering principles for a certain class of systems–to analyze and decompose complex interactions.

You could think of that tool as a kind of hammer. The temptation when you have a good hammer is to regard every problem as a nail. That’s my view of the Raymond Isbell approach to biological systems and biological origins: Every kind of biological complexity is to be analyzed in the same SE framework that applies to certain kinds of information technology computational systems. That SE framework is a truly wonderful hammer that has served you well, ergo biology is a nail.

I hope you find this helpful.

Chris Falter