Reaping the Whirlwind: protein function without stable structure


(Raymond Isbell) #102

But won’t versions 95-100 be around?


(Steve Schaffner) #103

Both.

No, not at all. Why would you think that? With rare exceptions, species don’t start with a single mutation; they arise from the accumulation of lots of different mutations that eventually make one population reproductively incompatible with another. Those mutations need only occur once, and they can be inherited by both males and females.

Depends on what you mean by a version. If you mean something like a new species, then no, by the time a population has evolved enough to be considered a different species, the old one is long gone. If you just mean that different versions possess different traits, then we do see the earlier versions. As you have probably noticed, not all members of a species are identical. Some of those traits are ones that are increasing in frequency because of selection.


(Steve Schaffner) #104

Your position was this:

That position is unambiguously wrong.

What’s limited about the scope? How many human genes do you think we have data on about their robustness to mutation?

We observe millions of changes. We observe individuals possessing those changes functioning just fine. Anyone arguing that those changes make functional organisms impossible – as you have been – is not talking about reality. What you need to do is stop trying to impose your intuitions on reality.


(Raymond Isbell) #105

It seem unlikely that a single or string of mutations will impact both male and female the same way. After all, the mutations must involve sexual function and that must impact male and female differently. I’m not saying it can’t happen, but again, it points to the unlikeliness of it happening. This seem to be a trend that I’m seeing in evolutionary arguments. They argue: “Well, it must happen this way.” But, the problem is that they can’t produce the detail to show that it does happen. Instead, they offer the end result as the proof which is begging the question. I challenged Steve Matheson on this when he claimed that every time a new offspring is born, it proves evolution.


(Raymond Isbell) #106

You can identify every protein in the cell along with its function, and how that function interplays with all the other proteins under all conditions? You understand the C4 functions that govern that interplay? You understand the functions of all the genes? Wow. You’re much farther along than I thought.

What I suspect you’re observing is simple correlation between a gene change and it’s final manifestation in the phenotype, ceteris paribus. If I built rockets with that kind of thinking without a deep understanding of all the other systems and their relationships, my career would end quickly.


(Steve Schaffner) #107

No. So what? We can identify every gene in the genome that codes for those proteins, as well as all of the noncoding regions in between and observe all of the variation that has occurred and is still occurring in all of them. We can determine that those variants are the result of random processes. We observe that organisms do just fine with those variants. These observations mean that organisms cannot be as brittle as you claim they have to be.

As it happens, we can also identify pretty much all of the proteins in an organism and all of the interactions between them, and then relate various characteristics of the protein, including its tolerance of mutation, to its role in that network.

If you tried to do biology with the attitude you’ve take here, your career would never start.


(Raymond Isbell) #108

How about the C4 functions that control all the proteins?


#109

What makes you think this? Males and females each contain the same set of 23 chromosomes and a mutation in any of these would impact both.


(Christy Hemphill) #110

One organism doesn’t give birth to a different species. Speciation happens over many generations at the level of populations. It’s a continuum where you can’t pick a point in history and draw a firm line between one species and the next at the level of a single generation. That would be like saying there was a moment in history when Old English became Middle English and the children of a certain generation spoke a different language than their parents.


(Christy Hemphill) #111

This thread from a while back has some good info about macro and micro evolution

This idea of co-evolving sexual compatibility has come up before, but I can’t remember where. It involves a pretty fundamental misconception about how speciation works. I’m pretty sure it is correct to say that as a population evolves there would be no parent generation that was reproductively incompatible with its offspring generation. The development of reproductive incompatibility requires isolating a population from the rest of its ancestor population either geographically or in an ecological niche. At first the isolated population reproduces among itself, not because it is impossible to reproduce with the members of the other population but because they aren’t available as mates. It’s only after a very long time of evolving separately that it becomes physically impossible for the two populations to interbreed. Plus, sometimes reproductive compatibility is more a matter of “taste” than biological possibility. Species that could interbreed and produce hybrids usually don’t because they don’t find each other appealing mates.


(Chris Falter) #112

You appear to be making stuff up as you go along, Raymond. A glance around at human populations, for example, would tell you that skin pigmentation mutations affect men and women approximately equally.

Biologists have in fact discovered, analyzed, and written peer reviewed articles about specific mutations in the human genome. The vast majority of them have approximately equal effects on both genders. Here are some examples from peer-reviewed literature:

  • lactase persistence
  • high-altitude adaptation
  • skin pigmentation
  • height

Your lack of familiarity with the voluminous evidence is astonishing, Raymond. Biologists have been carefully studying multiple classes of evidence for decades and using them to build mathematically persuasive primate phylogenies. Here are some classes of data that have been used in the mathematical derivation of primate phylogenies:

A real biologist could no doubt refer to more recent and more widely cited papers covering these and other classes of evidence. But these should help you realize that biologists are not indulging in circular reasoning when they speak about primate evolution.

I have read several books by YEC scientists with an academic background in geology, and I have read the RATE reports (both of them). I have also read quite a bit of literature from geologists who explain why the various radiometric dating methods are quite reliable. I have come to the conclusion that the YEC indictment of radiometric dating can be dismissed by the scientific community.

So I seriously doubt that someone with no academic training in geology (Chris Rupe, B.S. in biology) will tell me anything I have not already heard.

I am quite open to the idea that we cannot construct a phylogeny of all the austrolopithecine and hominid species from the past 8 million years with 100% confidence. There are limits to what we can learn from limited evidence. For example, in spite of exquisite technology and multiple camera angles, NFL replay officials were not 100% sure whether Julian Edelman touched the punt or not, and that is why New England is in the Super Bowl instead of the Chiefs. The officials actually knew quite a lot; anyone can see that the ball was within 1 cm ± 1 cm of Edelman’s hands.That was simply not enough confidence to overturn the call on the field.

So the fact that there is some uncertainty about some of the details regarding phylogenetic relationships in the hominid tree is completely unremarkable. But there are still things we can be confident about in primate phylogeny, just as we can be confident that the ball was at least extremely close to Edelman’s hands. The evidence of common ancestry is so strong (see my citations above) that I am 100% confident in the common ancestry of humans and chimps, and indeed of all primates.

Moreover, as someone who worked in software systems engineering and architecture for decades, I am quite sure that your analogizing between SE and biology is off the mark. Here are four reasons why your analogy is inapt:

  1. Many changes actually make systems more reliable. These kinds of changes are discussed in the refactoring literature. Uncle Bob and all that!
  2. Some kinds of changes are backwardly compatible and do not require synchronized deployment.
  3. Evolutionary algorithms can yield excellent solutions (i.e., identify at least local maxima) for a variety of problems. This is an important field of AI–Pedro Domingos identifies the evolutionary algorithm movement as one of the 4 “tribes” of AI.
  4. Microservice architectures with devops pipelines are highly adaptable to change. Facebook deploys 50 changes per day. Netflix and Amazon both deploy literally thousands of changes per day. This is a new school of system engineering that does not require massive coordination between hundreds of systems just to deploy one change. All of your assertions about the difficulty of introducing changes into complex systems are belied by the continuous deployment practices that Facebook, Netflix, Amazon, and many, many other businesses have been employing, quite successfully, for years in their extremely complex systems.

You seem not to have given any serious consideration as to how these four forces within the field of system engineering suggest that your analogies and conclusions are misplaced. You have restricted your thinking to the old-school, big, hierarchical systems with rigid interfaces that first emerged in the 70s. If you would be willing to think more broadly about the field of endeavor you and I share, you would realize:

  • biological systems can have microservice-style interactions,
  • they can have backwardly compatible changes, and
  • sometimes have simplifying, “refactoring” changes.

And let us not forget that they might even operate with something like an evolutionary algorithm, too!

The theory of evolution includes directional components like competition and habitat that get summarized in the term “natural selection.” In other words, there are forces that shape the direction of change; it’s not just random.

Raymond, when you stride into the debate hall and proclaim everyone else to be ignorant chumps–while you make astonishingly wild, inaccurate statements that are easily refuted by a casual glance at the biological literature–you are not building a very good case for your credibility.

And when you ignore the obvious implications of recent developments in the field of systems engineering–the field that you have chosen as your point of departure for reasoning about change–I think you need to do what Brooks suggested for 70s-style systems that have become brittle:

Throw out your unproductive, brittle way of thinking about the problem, and familiarize yourself with the data and findings of the scientists who have collectively spent hundreds of millenia studying and writing about evolutionary biology.

If you’re passionate about the field of study, and are willing to learn before you preach, you can no doubt make great strides. It will probably take years–it took me about two decades, honestly.

Regards,
Chris Falter


(Steve Schaffner) #113

Everything here is great except this. The call on the field was that he did touch the ball, and the call was overturned. You clearly haven’t been studying the literature on this subject. . .


(Chris Falter) #114

A Patriots fan roars!


(Steve Schaffner) #115

Just stating the facts, that’s all. Now it’s true that if we calculate the probability of the ball missing Edelman by chance, we’ll find that it was vanishingly small, and that therefore an intelligent designer must have been involved, one that favors the Patriots. But that’s not my fault – we just have to follow the data wherever they lead.


(Raymond Isbell) #116

Wow. You guys use big clubs when you beat people down who don’t agree with you. You cite peer reviewed literature, experiments, narratives, and the kitchen sink as you try to build an impressive put-down of those who challenge you. I am tempted to address each of your points above, but at my age I’ve accumulated enough wisdom to know it would not bring us into agreement. I stand by what I say, and what really amazes me is how you guys persist with your certainty about evolution given your understanding of how complex the cell is. I’ve yet to hear from any of you regarding my mention of the C4 functionality that is necessarily active thru-out the cell. The reason you don’t address it is that you don’t know how or where it’s hosted, how it works, etc. It’s the orchestra director of the cell and it’s the cell’s operations chief, yet you have no idea how it is instantiated or how it’s controlled or how it controls. It’s the heart of the cell and yet you will not even consider that your ignorance of it should give you pause. There’s so much going on in the cell that you don’t understand, yet your certainty that it functions based on the neo-Darwinian mechanism is breathtaking. We never got into the irreducible complexity argument which I wanted to discuss with you guys, but I think it would go the same way as our earlier discussion have gone. By the way, it’s obvious that all the little molecular machines get built up again and again each time a cell divides. The ATP Synthase Enzyme comes to mind much as the Behe’s flagellum motor? What orders, delivers, positions, brings to bear the correct tool to make each action in the assembly process perform at the right time, places the partially assembled parts waiting for the next step in a waiting cue, calls it up when needed for the next step, notifies the Executive Controller that orchestrates the process and advances the assembly to the next step in construction, and notifies the tools (proteins) and parts needed for that next step? Where is the assembly plan and the trigger that initiates it at the correct time? Where is the navigation plan for all the parts and tools needed to complete the assembly, and how is that navigation data generated, communicated, received by the tools and parts, and executed so they arrive at the needed location at the right time? I’ve spent some time reading up on what they know about the construction of ATP enzyme and the flagellum motor. I’m more astonished at how much they don’t know. Yet you guys are sure that it evolved by random mutation filtered by natural selection. I assume you believe the assembly process also evolved. That’s stunning. What I’ve seen so far is that evolution is a house of cards, an impressive one at that, i.e., it looks impressive with its argot. And there’s no shortage of devotees. I’m equally baffled at how you reject the argument put forth by the ID group that design is easily recognizable. Maybe God designed us that way (that is to be able to see it easily) so that when we complain at our judgment, he’ll politely tells that our embracing evolution was a choice we made and without His help. He’ll remind us that the facts were in plain sight, but we chose to embrace “other facts.” Is that what the Bible calls idolatry? How will you answer him? Will you cite the EC peer reviewed literature? Will you tell Him he doesn’t understand biology? He might indeed agree with you since the biology you’ve conjured up is full of circular reasoning. Your embracing evolution is like one who stares at Mt Rushmore and believes that wind, rain, freezing and thawing eroded the 4 faces of the Presidents into the mountain side. How do you answer that? All I can say is “How do you not see it?”


(Mervin Bitikofer) #117

It’s called data. And it only looks “threatening” to those who don’t like the most successful interpretations of it.

Nobody here has been trying to “put you down” -or if they have [I haven’t read every last word above] then I apologize on their behalf. But I know these folks who you’ve been interacting with enough to know they take pleasure in helping spread understanding - even to those who disagree with them. At the very least, even if your disagreement persists, you should still be grateful for the opportunity to have your arguments sharpened and maybe at least discard some of them that just don’t work. They would expect the same, if you proposed things that helped make even better sense of the data we have - they would want to know so they could also sharpen (or change) their own arguments accordingly. I.D. has failed thus far to do this.

I can tell you don’t want to hold on to straw-man caricatures of evolution, though you lapse back (as with your Mt. Rushmore example) which still shows a persistent misunderstanding on your part. But in other of your correspondence I gather you really do show interest (when frustrations don’t get in the way) in climbing that ladder to better understanding. And for that I commend you.


#118

@Raymond_Isbell you have fallen into the “evolution = atheism” trap. I know God is the designer because the Bible tells me so. I don’t depend on “detecting design” to know this. What do you call someone who depends on their own ability instead of taking the Bible at face value?


(Christy Hemphill) #119

Do you think there may be a difference between recognizable and scientifically demonstrable? I think God designed creation. I don’t think science can demonstrate that since the tools of science are not adequate for explaining divine activity.

There is no “EC peer reviewed literature,” there is just science. And for Christians, God is the God of science and no truth that we can uncover about the world he made is threatening to God or takes away from his rule over the world. So evolution and the piles of facts that back it up shouldn’t be threatening to our faith either. I think God would take delight in his children using the brains he gave them to explore the world he put them in.


(Phil) #120

I really don’t think he will care what we think about evolution. He said as much when he related what we will be accountable for in Matthew:
34 “Then the King will say to those on his right,…(you know what goes in the blanks so I will save the bandwidth)…

40 “The King will reply, ‘Truly I tell you, whatever you did for one of the least of these brothers and sisters of mine, you did for me.’


(Dennis Venema) #121

There’s a whole field devoted to these sorts of questions - developmental biology. And we know a whole lot about how these processes work. You’ll have to add studying developmental biology to your list along with evolution and population genetics.

Your argument is basically an argument from personal incredulity. But it’s not an informed incredulity. It all seems impossible to you, but to scientists (and even informed laypersons) it’s not impossible. It’s accomplished by well-understood mechanisms. We don’t know every detail, of course, but we have a good understanding of the main principles and mechanisms that accomplish these events.