Reaping the Whirlwind: protein function without stable structure


(T J Runyon) #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.


#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.


(Raymond Isbell) #305

Makes for good eisegesis, though!


(Ryan Bebej) #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.


(Chris Falter) #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.


(Chris Falter) #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?


(T J Runyon) #309

Would love to! YouTube?


(Ryan Bebej) #310

I gave a longer presentation about this in the Christian Perspectives in Science seminar series at Calvin a couple of years ago (audio, slides) and a shorter one at the BioLogos Evolution and Christian Faith conference in 2015 (audio). Enjoy my sweet and soothing dulcet tones!


(Raymond Isbell) #311

I think you got me on this one. I recall Meyer mentioned it in a video so maybe there was an exception. I can’t prove it, but it struck me as odd when I heard it. That’s why I remembered it. But this is not the real issue anyway. We need to focus on evidence. I’m starting to see where the weakness in evolution really lies. It’s in its evidence that barely qualifies as evidence at least from a scientific standpoint. If I used that kind of evidence to prove to my Project Manager that my machine was ready for operations, I’d be fired.


(Randy) #312

Dear Mr Isbell,

Thank you for your patience with me. I apologize that I think I misunderstood. Yes, we should think of every possible use of a given part. However, I think that in the long run, the multiple paths and evidences of scars from development (not just physiology and anatomy, but erosion/geology, astronomy, and other areas) converge to make an overwhelming case for evolution and an old earth. However, I think I misunderstood the reason for the verse. In some cases, it’s been used as a way to sidestep an issue–which I don’t think you are doing here.

As for context, I want to read it more, but it appears that God is calling people to repentance–and that chasing after their own selfish ways is what he’s asking them to give up. He’s not asking us to deny the evidence of our eyes. The most extreme example comes up in my own church (the people of which I love dearly)–the omphalos hypothesis–that God created everything, scars and all, to appear old. The way they understand it is that the age is actually maturity. However, things like fault in the crust with extrapolated ages on multiple fronts, etc, are overwhelming to me–like saying God gave Adam a bellybutton to look mature. I don’t think you were saying God goes that far; you are just asking for careful consideration.

Here are several aspect of your general approach which I appreciate, and which can be found in this article from last year by the philosopher Jen Zamzow:

You, first of all, start with “shared values and shared experiences.” You agree that evolutionists can be Christian, and vice versa. You also agree that we can all struggle through the morass of a very complex universe.

Second, you try to put yourself in another’s shoes.

Third, you critique ideas, not individuals. It’s very easy to fall into the other trap. You are doing well with avoiding that.

Four, you choose curiosity over certainty.

This all reminds me that with the great complexity of what we set out to learn, we are all going to appear to the other side as not fully grasping, or even trying to grasp, the whole truth. If it took me at least a decade to come to where I am now, I am sure that those who taught me thought I was bullheaded. It was actually two or three atheist/agnostic professors in undergrad who, primarily with their patience and kindness, helped me understand better. They were not ready to criticize me or my faith, or personal intent–just to gently ask questions. And I’ve greatly appreciated interacting with others, such as the moderators here, to help me muddle through some thorny questions. I still have a long way to go. I

Anyway, what I what to emphasize is, we all come to this with prejudices and teachings that we hold dear. It takes a long time to change–and that doesn’t mean that in the meantime, we are purposely avoiding truth. In fact, pushing too hard will only result in discomfort and guarding. It means we need more patience and understanding–just as my skeptical professors and other godly Christians with better science insight have aided me.

Thanks, and I appreciate your patience with me.

God bless.


(Chris Falter) #313

I agree with your general approach–we do need to focus on the evidence. Does this mean that you would be willing to set aside the question of whether SE principles should be applied directly and in toto to biological origins–at least for the time being?

Just to clarify: I am not asking you to abandon that issue until kingdom come (unless you are so inclined :slight_smile:) . I am only asking if you are willing to set it aside for now so we can move onto what might be more fruitful avenues of inquiry such as genetic sequence analysis, population genetics, radiometric dating techniques, and such.

Yours,
Chris Falter


(Raymond Isbell) #314

Hopefully, I didn’t say or imply this. What I meant was that using what we (humans) think is unreasonable is probably not a good criteria for judging evidence. It’s more likely that our information and understanding of what we observe is deficient. Thus, caution should be observed when making a claim that the design of some structure in the cell is bad and warrants a negative conclusion about God’s involvement.

As I’ve said recently, the central issue seems to be one of how we assess evidence. In that regard, I’ve begun to notice that evidence adduced in support of evolution seems questionable that it’s even evidence to being with. Saying evidence under review “MAY account for” is much different than saying that evidence “accounts for.” The word MAY is rightly used to point out that the evidence is “consistent with” as opposed to the evidence is “conclusive.” Dennis Venema’s video and several of the papers I read supporting evolution were consistent in their staying away from words that suggested the evidence was conclusive and provably correct. What seems to build evolutionist’s confidence in their view is that they have lots of examples of evidence that “MAY account for” and “is consistent with,” but none that say “proves.” Is that significant? I think so.

In the engineering world that I know, words like “is consistent with” or “may account for” are the first sign a design has problems. It first implies we don’t sufficiently understand it, and second it means we’ve yet to produce a set of hypothesis/predictions/tests that will ensure that every failure modality has been identified, and a mitigation plan has been provided, tested and confirmed. Instead, it means that a carefully prepared error budget is in place that reflects acceptable levels of risk in all categories that affect the mission. (This mission is answering the question, “Is evolution the best explanation for the observed evidence or is ID or YEC a better explanation?”

Should I not apply this same rigor to my assessment of the evolution vs ID vs Creationism question? For each, what are the failure modalities? Lack of evidence? Quality of the evidence? Consistency of the evidence? Support of the evidence? Analysis of the evidence? Are the hypothesis and predictions testable with tests that are valid, i.e., do we know that there’s sufficient evidence available to perform the test that will provide a definitive result? If not, what reasoning can be applied to the evidence we do have that will enable us to render a decision with high confidence? Are there political considerations in play that color the way I view the evidence? Will I lose my job and jeopardize my career if I embrace ID or YEC? For me intellectual honesty demands that I get answers to these questions before I draw a conclusion. Self-deception can come into play when I choose to ignore any of these considerations. What are the risks in making a bad decision? If evolution is false and we as Christians embrace it, we in effect are siding with the unbelieving world and giving Christianity a black eye in front of God and the angels who are said to be observing us with high interest. Will that bring God the glory he seeks and deserves?
Clearly our stance is of high importance, and it deserves a careful, critical, and complete examination. Are you ready to rumble?


(Stephen Matheson) #315

All my life I have been taught that the Nile Delta was created by the deposition of sediment by the Nile River, over millennia. Apparently this theory accounts for lots of evidence. Apparently all the evidence is consistent with the theory. But none of these examples of evidence says “proves.” Same goes for the volcanic origin of the mountains in Arizona, where I was just visiting family. Same goes for the glacial origin of the Great Lakes, where I lived for awhile. Same goes for the formation of the Himalayas. And so on.

Then there are examples from developmental biology. A tiny handful of experiments have shown that a single-cell human embryo can grow into a fetus. All of the people participating in this forum appear to be adult humans, who we surmise were once fetuses that arose from single-cell embryos (that formed from fusion of oocytes and sperm). This theory, that BL forum participants arose from zygotes, explains relatively little in the way of observations. All it really does is stand in opposition to other theories, such as instantaneous creation last Thursday or spontaneous generation of a homunculus at the moment of quickening. It’s true that all the evidence is consistent with the theory, but there is no decisive evidence for the zygote theory in any of the cases. If we conclude that the theory is not “proven,” we would be correct by some definitions of ‘prove.’

Arguments based on the definition of science, or the definition of “proof,” are the last refuge of the creationist.


(Chris Falter) #316

You can take a Marine out of the battle, but you can never take the battle out of a Marine. :wink:

Thanks for your service, BTW. Our country is better because of the sacrifices that you and your cohort made on our behalf. My uncle flew choppers in 'Nam, but he doesn’t like to talk about it.

As we think about the journey ahead, let’s step back, take a deep breath, and prepare for a lot of hard work. Let’s keep foremost in our minds the counsel of Scripture found in Proverbs 18:17 -

The first to plead his case seems right,
Until another comes and examines him.

I have often violated this counsel myself. And every day we see plenty of people who who violate this counsel, don’t we?

Here’s an example I saw recently: A very intelligent man read a lengthy book on the topic of hominid evolution and radiometric dating. The book was well-written, cogently argued, and had numerous citations to scientific literature. Highly impressed, he went to Amazon and wrote a glowing review of the book. In other words, he had not put Proverbs 18:17 into practice.

Because the man had no prior experience in the fields of hominid evolution and radiometric dating, he he had no knowledge of the vast amounts of contrary evidence and techniques that had accumulated within a truth-seeking community of experts in those fields. Those experts have for centuries maintained a rigorous set of community standards with respect to experimental procedures and publication, and they have been working hard to root out those who do not share their rigorous standards. Consequently, the community is confident that their approximations of natural history are getting closer and closer to the mark as they continue working collaboratively.

Now the book did not in the least conform to those rigorous standards. None of its contents were submitted for peer review. Peer review could have helped the authors take into account evidence they had not considered, to take into account the probabilistic distribution of measurement errors, and so forth. Unfortunately, the authors were not interested in getting that kind of feedback before they pushed their book into print.

Those who strongly value the rigorous standards of experimental procedure and peer review of the scientific community are therefore quite skeptical of the book’s claims. They have seen too many other authors with no commitment to peer review make basically identical claims that turned out to be entirely implausible.

On the other hand, actions have effects, so the man who enthusiastically wrote the book review while ignoring the counsel of Proverbs 18:17 now finds himself emotionally committed to defending the viewpoint of the book. Can he extract himself from this quagmire?

I think he can–in fact, I’m sure he can. The reason is that I also found myself stuck, unknowingly, in such a quagmire 30 years ago. The turning point occurred when I stopped inveighing against the supposed inaccuracies of radiometric dating and supposed circular reasoning of the theory of evolution, and started listening to friends who were familiar with the evidence that the expert community had accumulated.

Yours,
Chris


#317

@Raymond_Isbell Did Christian doctors who treated patients before the Germ Theory was established give Christianity a black eye for believing something that wasn’t true? Why would accepting the evidence that shows evolution is currently the best explanation, even if it doesn’t rise to some level of proof, possible cause anyone to acquire a black eye? This sounds like you have fallen for the “evil evolution” trap promoted by some Christians.


(Jay Johnson) #318

Now, this makes perfect sense, and it also illustrates the problem that I mentioned previously, which is that we Christians are gullible people. We take Meyer’s excuse at face value because he’s on “our team,” and we have a presumption that Christians should respect the truth. That’s obviously not always true, especially where money, celebrity, and massive egos are involved. If you want to make progress, stop taking Christian apologists at their word. Do you not recall what Jesus said about false prophets? Fame and money are their gods, and when the truth gets in the way of that, the truth soon enough will be found wearing cement overshoes at the bottom of the river. Test everything. Hold fast what is good.

Actually, none of its contents went through the normal process of editing/fact checking that even non-academic books endure. The publisher of Contested Bones is FMS Publications, which is another name for Feed My Sheep, a 501-c-(3) started by the author, John Sanford. His co-author, Rupe, is an employee of the organization. In short, it’s a more sophisticated version of self-publishing.

You’re not in the engineering world anymore, Raymond. Science does not proceed in the real world as you imagine it. The language that you complain about is actually standard practice in academic journals and books in all disciplines, not just evolutionary biology. Take a look at this article describing the link between Alzheimer’s and the bacteria that causes gingivitis:


The last sentence of the abstract reads: “These data suggest that gingipain inhibitors could be valuable for treating P. gingivalis brain colonization and neurodegeneration in Alzheimer’s disease.”

You’re taking language that is standard practice in every scientific discipline and trying to give it special significance when it is used in reference to evolution.

I could go on, but let’s try this. Since @sfmatheson is the Editor in Chief of a scientific journal, I’d like to ask how he would react if I sent in a paper that claimed “conclusive” and “definitive” proof of my hypothesis. (Edit: Okay, his first reaction would be to send it back because I have no credentials. But, suspending disbelief for just a second …)

Uh oh. Never should’ve mentioned that out loud with me in the room, bro. I could start asking for favors any minute now … :wink:


(Stephen Matheson) #319

Great question. This almost never happens because “proof” is a word used rarely by biologists and, I suspect, by scientists in most disciplines. It’s not the right way to talk, and it’s not the right way to think. This is essentially universal intellectual practice, at least in biology.

But more generally, overstatements about the impact of one’s results are pretty common in papers we see, and we and many other journals require claims to be stated accurately. (Some journals have very strict policies about language associated with overselling, such as “surprisingly” and “strikingly” and so on. We’re a bit more relaxed on that, but tackle it on a case-by-case basis.) Such papers are almost never rejected on that basis. Instead, the hyping is addressed either during review (reviewers can and should critique such things) or after the paper has been accepted but before publication. In your example, “proof” would be removed (at our request), and “conclusive” or “definitive” examined very critically but probably removed.

This all assumes that the paper wasn’t judged to be non-credible at the start, and massive overhyping by the use of “definitive proof” (for example) is a significant red flag.


(Jay Johnson) #320

Great answer. Thanks. It seems that the red flags are actually flapping in the opposite direction than @Raymond_Isbell would expect. The more definite and certain are the language and conclusions, the more cautious we should be about the actual evidence.


(Steve Schaffner) #321

Experimental particle physics has an informal policy that a result with 3 sigma significance is referred to as “evidence for”, while 5 sigma significance entitles you to announce a “discovery” or “observation” of a particle or process.

Looking on Google Scholar, however, I see that some papers do indeed claim “definitive proof” of this or that, even in biology. That just strikes me as bizarre wording.