Reaping the Whirlwind: protein function without stable structure


Try these.


Exactly. What looks like a drunken walk to us is just God having things exactly as He desires. We don’t know His mind so who are we to criticize how He accomplishes the task?

(Raymond Isbell) #84

Thanks. That should be interesting reading.



Actually, Steve Matheson told you all you need to know in his very first reply to you:
"The notion that one little change requires some epic “coordination” to avoid catastrophe… is falsified every time an animal (including a human) produces live offspring. "

What he didn’t spell out (perhaps because he didn’t realize how ignorant you are of basic biology) is that “every time an animal…produces live offspring”, the offspring inherit an appreciable number of essentially random mutations which come about during the reproductive process. For instance, your genome has around fifty (give or take) mutations relative to your parents’ genomes. These are not simply the normal reshuffling associated with sexual recombination, but bona fide, de novo alterations, such as altered base pairs. And these mutations accumulate, generation after generation, so you have some 200 mutations relative to the genomes of your great-great parents. And that is true for all 7 billion humans on the planet.

Would making 200 random changes in a typical computer program almost certainly wreck it? YES.
Does making 200 random changes in the human genome almost certainly wreck it? NO. [1]
So your analogizing with human computer programming and systems engineering is simply not valid.

You can accept this reality, and read the references given to you above in order learn more details on the robustness of biological systems (relative to human-designed systems) or you can keep on insisting evolution violates (human-designed) SE principles. Your choice.

[1] Just to nuance this statement a bit: Most conceived human embryos and babies do fine with their accumulated mutational load. But not all. As I recall, something like 40% of fertilized eggs end in spontaneous abortions (miscarriages), due at least In part to genetic problems, and something like 3% of live births result in children with some identified genetic defect (inherited medical condition). Thus, biological systems are quite robust (much more so than a typical computer program), but not 100%.

(Stephen Matheson) #86


Thanks for trying.

(Stephen Matheson) #87

The actually interesting and currently unanswered question is quite the opposite of what @Raymond_Isbell has asserted. Humans (and many other animals) experience relatively high mutation rates. The implication is that mutations are accumulating in the human population, and because some subset of these mutations is deleterious to some extent, the genetic load (burden of disadvantageous genetic elements) should become dangerous to the population. (The really bad mutations are weeded right out, but lots of moderately or weakly disadvantageous variants will stay.) But… news flash… we’re not dead. Why not?

People are working on this question as we speak (I know one of them really well). Epistasis is one big obvious potential answer, and a major paper a couple of years ago (below) made a strong case for it, but apparently it’s not necessarily the complete story.

The basic message is that the belief that mutations will destroy the human genome is a belief so far from accurate that it can be completely inverted logically to yield an actual ongoing research question.

(Raymond Isbell) #88

I read them both, and didn’t find them to be convincing either in support of evolution or ID. There’s wiggle room in both. The examples are just not clear cut enough to resolve the issue.

(Raymond Isbell) #89

I know you don’t want to offend, and if I were a snowflake, I might get offended when I read a phrase like “he didn’t realize how ignorant you are of basic biology.” You may not realize it, but I think you guys are beating me up much worse than I am beating you up. Steve Schaffner noted that I was pretty strong in my challenges. I accepted it and am trying to do better. That said, it’s becoming more obvious to me that you guys don’t really understand the engineering principles that I’m trying to convey. You claim you do, but post like yours and Steve Matheson tell me otherwise. The cell is an engineering marvel, and everything that goes on in the cell follows the laws of physics. SE provides an organized framework in which to view it. That organization allows one to see order, structure, and ensure that the laws of physics are not being violated. That’s why designers use it. It keeps up from designing junk that will fail. Some of the claims you guys are making sound like magic, and a way to avoid having to deal with the details that scientific laws and principles impose. Certainly, I don’t know biology that well, but I do understand the physics behind much of what I’m seeing as I learn, e.g., DNA specifying and building proteins. I suspect that I also see much that you don’t see, e.g., the need, but still unknown, command, control, communications, and computing (information management) that’s going on to support all the activities in the cell.

Yes, there’s clearly an impressive capability within the genome to accommodate changes. (I’ve learned that from you guys and I’m grateful for it.) The question is, however, does that accommodation come from random or designed modification. Having learned from you guys about the robustness, flexibility, and redundancy that’s obviously built into the cell (you think evolution provided it, and I suspect that design provided it), I’m actually more impressed at the marvel of the design. That kind of functionality is even less likely than if it were not there. In fact, the probability of that kind of functionality randomly coming into the genome is many orders of magnitude less likely than without it. The level of coordination across all the cell subsystems would be much greater if you’re building into it these capabilities (robustness, flexibility, and redundancy). The way you worded your description of 200 random changes wrecking a computer program is spot on. However, I could design in the robustness, flexibility, and redundancy to make a computer program much more “fault tolerant.” (The cell is clearly fault tolerant.) Fault tolerance is often a design requirement particularly in systems where failure is costly. It’s expensive to include fault tolerance, but it may be more expensive to have a higher failure rate of the system. Again, it all goes back to the system’s mission. (In evolution, there is no mission if I understand evolution.) If human lives depend on it, you can be sure a big part of the budget will be devoted to building in fault tolerance. Failure mode analysis and fault tolerance is an important element of designing a large system-of-systems. I took a course in grad school titled “Probabilistic Systems in Engineering Science” where we learned to model systems with random variables. The purpose of the course was to teach us how to estimate and address the likelihood of failure in a system. Some of the probability density functions (PDFs) had a high level of kurtosis (relatively flat so that choosing design parameters was not cut and dry.) In those cases, you must be really careful in the failure mode analysis and design of fault tolerance. That you have that in the cell is truly impressive. To conclude it came about by chance and natural selection really challenges credulity.


@Raymond_Isbell you appear to be a Christian that currently finds ID persuasive. Am I correct?

If so I would like to ask you how you see God fitting in with ID.

(Chris Falter) #91

But not the ape species that were alive 7 million years ago (or so) when the austalopithecus and chimpanzee lines diverged from a common ancestral population.

The ape species of today are significantly different from the ape species of 7mya.

Chris Falter

(Chris Falter) #92

Hi Raymond,

Many changes in a “system of systems” are introduced in a backwards compatible manner, right?

Is it impossible for biological changes to occur in a backwards compatible manner?

Chris Falter


How does, “if evolution is true, why are there still apes”, remain a thing in 2019?

(Raymond Isbell) #94

Your statement is solid support for an unproven theory. What I’m finding consistently among those supporting evolution is that there’s a lot of circular reasoning going on. You use as starting points assumptions that an evolutionary transition is true and then deduce the truth of another claim that you say is proven because your first assumption is true. You are doing this when you say the Ape I referred to comes from a different branch in the Phylogenetic tree. That’s the “begging the question” fallacy. Your claim above is true only if the tree is true. But that tree is an explanation that is full of holes tied together with unproven assumptions. The tree is supposedly supported by the fossil record, but that also is full of unproven assumptions and extrapolations. If you look closely you see a great deal of missing data that could settle the question. However, the reality is that the proofs offered by evolutionists consists of pictures that are not much more that what you see from a sixth grader’s show and tell presentation. They’re a far cry from being considered scientific. Many evolutionists start their arguments by assuming those pictures prove their point so that further arguments building on that are true. I’m sure you’ve heard of read Jonathan Wells books on Icons of Evolution which show my point.

I would suggest you also read the recent book titled “Contested Bones” by Chris Rupe and John Sanford. It will show clearly my point. It also has one of the best treatments I’ve seen on radiometric dating. It’s a real eye opener for those who are honestly looking to assess the other side of the debate. Remember, intellectual honesty demands that you give both sides of the debate a fair hearing. That’s what I’m doing. I really want to hear your best arguments for evolution. If you are correct, I’ll publicly acknowledge it. I’m going to give it an honest effort.

My background as a Systems Engineer and Research Scientist working in the field of AI applied to imaging science tells me that there’s lot of detail missing from this debate, and both sides know it. How is that we can come to such firm conclusions when we don’t have all the facts, and worse, we’re all acutely aware we don’t have all the facts. Yet evolutionists seem to ignore their “ignorance” (I don’t mean that in a pejorative manner. There’s much neither of us know.) and proclaim evolution to be true. Sadly, they even resort to mocking the other side. That’s a strategy employed mostly by politicians, but I’m seeing lots of it among evolutionists. I really don’t understand it. Most of us are well trained in the sciences and should be equipped to objectively reason our way thru evidence and come to a common conclusion. Instead, we get into ad hominem attacks, mocking, and other unprofessional tactics to win our arguments. If we’re Christians, as I am, we should try to avoid that, and treat each other with respect and dignity.

(Raymond Isbell) #95

I think I addressed this in one of my early posts where I addressed “Change Management.” Most of a systems life cycle costs are in this area of work. It’s a tough problem, and more than any other, it requires design expertise and knowledge of the existing system. Most SEs would laugh if you told them that a system will “self-modify” by chance. There was book published in the 1970’s and still available titled “The Mythical Man-Month by Fred Brooks” that addresses the challenges of software engineering. One conclusion was that complex software becomes harder to maintain with each successive modification. The side effects of every change are never fully anticipated and the result is unstable software with too many patches in it. Eventually, it becomes cheaper to throw it away and build a new one from scratch. It’s all because of the interdependence of the many subsystems. It illustrates nicely my initial thesis that change must be coordinated across all the subsystems before it will function in a new and better way. Humans have proven we can’t do it to our most complex software systems. We rarely know and understand all the complex relationships among the various subsystems, and to make things worse, often the experts for one subsystem don’t know how the other subsystems work so they have no clue as to how a change in one subsystem will impact the others. To think that all that change will happen by chance strains credulity. Maybe now you can begin to see why I’m skeptical of neo-Darwinian evolution.

(Raymond Isbell) #96

Sorry, but I’m not sure I understand your question.

(Steve Schaffner) #97

We do. We see traits increasing in frequency because of selection.

As I already said, version 1 is not alive. As others have pointed out, “ape” is not a species. Darwinian evolution involves the replacement of less fit traits by more fit traits. Once that happens, the less fit trait isn’t there anymore, pretty much by definition. If the ancestral population splits into two and one branch evolves into version 100, the other branch is going to keep evolving, too, into version b, c, d, … Different traits may change on the two branches, but the original population will not exist when you reach version 100.


@Raymond _Isbell,
Re : “Yes, there’s clearly an impressive capability within the genome to accommodate changes. (I’ve learned that from you guys and I’m grateful for it.) The question is, however, does that accommodation come from random or designed modification. Having learned from you guys about the robustness, flexibility, and redundancy that’s obviously built into the cell (you think evolution provided it, and I suspect that design provided it), I’m actually more impressed at the marvel of the design… To conclude it came about by chance and natural selection really challenges credulity.”

So, it seems that you now do acknowledge that genomes of living things are indeed robust enough to handle random mutations, some of which will cause identifiable changes in expressed proteins. Thus, your earliest objection, that evolution (via random mutations and natural selection) is impossible, seems to have been resolved.

Your more recent concern, a snip of which I cited above here, seems to be with the ORIGIN of living things, presumably the origin of the first living cells, which possessed the type of robustness that we observe in both single-celled and multi-celled organisms today. Once those cells are going, then evolution can take off, and indeed, there is vast evidence that all of today’s biota developed from single-celled ancestors over the past several billion years. Biological evolution takes those first living cells as a starting point. But how these cells came about is actually a different issue or subject than evolution. This is typically called “abiogenesis”, rather than evolution.

The abiotic origin of the first cells from plain chemicals is very poorly understood. People here have given you detailed reference after reference meeting your other objections, but I think the data trail starts to peter out when we push that far back in time. If you want to claim that this origin could not have occurred by natural processes (and thus the intervention of an Intelligent Agent is required to fill that gap), so be it.

(Raymond Isbell) #99

Sorry for the delay in responding to this question. It seems a little off our track and suggests that I’m being set up for an ad hominem attack. Regardless, here’s a quick answer. I am a Christian. I define that as one who believes that Jesus Christ is the architect, creator, and sustainer of the universe where we live. I’m formally trained in the sciences (engineering mostly (Stanford undergrad, Stanford and Naval Postgraduate School grad)), and theology. I went to a protestant seminary to learn the languages and systematic theology. Much of the way they teach application of theology seems wrong so I chose not to pursue it further. Theologically, I fall into the Free Grace Camp (not Arminian and not Calvinist). Free Grace simply says that Christ’s atoning work on the cross was sufficient to save all men if they simply accept it as true (believe it). It’s not only easy believism, but free believism. Salvation can’t be lost, once received. Once you believe and become part of the family, the job is to transform your thinking from a worldly viewpoint to a divine one. (Most Christians today are still in the worldly thinking mode.) Eph 2:7 is a good summary of why God created us in the first place. Grace is the better way and God wants us to know it and live it both for our benefit and to demonstrate it to the Angels. That takes time and learning scripture (faith comes by hearing….Rom 10).

As to God’s fitting in with ID, He (Jesus Christ) is the designer. He’s very intelligent and has the power to do anything that we can imagine, e.g., speak the universe into existance. You don’t want to be on his bad side when you enter eternity. Christ controls history down to the smallest level of detail. Regarding predestination and election, I see the Molinist view to be the one that explains it with the fewest problems.

One area of the cell that I find intriguing is what I termed earlier as the suite of C4 functions (Command, Control, Communications, and Computing) that are obviously at play, but our current understanding of biology hasn’t identified it yet except for a very small portion. C4 functions appear to exist at multiple levels in the cell, e.g., how does a protein know what to do, when, where (and how to get there), when to stop, etc. and do so in coordination with all other functions. (The concept of a critical path comes into play and something you must understand if you are to find the answers.) How are sensor inputs processed, communicated, interpreted, and integrated into larger sets of function in the cell. These are standard questions that any SE will ask. SE’s don’t advocate theories until they understand these basics. SE’s do, however, recognize design when they see it. They also look deeper for explanations before they draw conclusions such as the whale came from a hippo. 6th grade show and tell pictures aren’t sufficient. SE’s know the importance of detail and know when to reserve judgment until they identify and understand that detail. I’m an SE in search of detail would be a nice summary of my position.

(Raymond Isbell) #100

Are we seeing “Micro” or “Macro” evolution? A new species (Macro) suggests that both male and female instances of a specie must mutate independently and together if they are to become a new specie capable of reproduction sufficiently different so that other species can’t interbreed? I’m sure this is an old question that has many attempts at answers, but as the old saying in the South goes, “Those dogs don’t hunt!”

(Raymond Isbell) #101

I think you overstated my position. There’s no question that we see robustness in the genome. The question regards its scope. The very limited scope observed so far is hardly resolves the issue. I don’t think we can say it’s resolved until we identify all the changes that must accompany those that we observe and can show that the integrated whole (all the changes) functions as you claim. There’s still a lot of work to do before I’ll agree that it’s resolved.

In all of my discussions so far, I have not brought up the abiogenesis question. You’ve seen a number of stochastic models offered to refute the secular theories, and they all provide very unlikely outcomes for that possibility. If SE were integrated into those models, the numbers would show it to be even less likely. So I’m not talking about abiogenesis. Instead, I’m focusing on neo-Darwinian evolution.