Reaping the Whirlwind: protein function without stable structure


#41

@Raymond_Isbell Perhaps this take on your idea will help you to see what you are missing.

The sub-systems in each person are the results of their unique DNA. The DNA is the blueprint/specification (I really don’t like this analogy) used to build the sub-system.

When off spring are formed their DNA is the result of the joining of the DNA from both parents. This DNA is again unique. Now in the vast majority of time the results of this new, unique DNA is a healthy, bouncing baby person.

Could you, as a SE expert, build two different and unique systems that are both fully functional and then take a random mixture of the sub-systems and have the resulting system-of-systems also be a fully functional, unique system? BTW, this mixture might be missing some of the sub-systems, might have non-functional sub-systems, or even contain duplicates of some of the sub-systems.

Also every person born has a limited number of mutations (bad specs) and yet the person is normally fully functional.


(Raymond Isbell) #42

Thanks Bill. You used an acronym I don’t recognize: EC. Does it mean Evolutionary Creation? I’m still trying to find out what you guys actually believe. I know that Hugh Ross embraces the Big Bang Theory, and I’m sure ya’ll have an argument to counter the charge that it violates at least one physical law (1st Law of Thermo). I would love to read any exchanges you’ve had with critics on the big bang. If however, you don’t have an issue with the Big Bang being outside EC, then disregard.


(Christy Hemphill) #43

Yes. EC=Evolutionary Creation which is preferred for various reasons over TE, theistic evolution.

Most EC proponents accept mainstream scientific consensus, which would include Big Bang cosmology, standard geologic ages, and evolution as the best model explaining the diversity of life. Where EC people have the most intramural debate is probably “what to do with Adam and Eve” “how does God’s sovereignty work with freedom in nature” and “how did the first life originate-miracle or ‘natural’ events.”


#44

Start here.

There are more sources on the Resources page.

The argument is usually the 2nd Law of Thermodynamics and as an Engineer you should be aware of why that law wouldn’t apply.


(Christy Hemphill) #45

An article

@pevaquark Do you remember any good Big Bang threads from the past, or any good resources on this? I looked, but most of the ones I found you have to wade through quite a bit to get to informative parts.


(Raymond Isbell) #46

Let me try to explain my quandary over your charge that I’m using a strawman. First, it’s a deceptive tactic used to discredit another’s position. Second, it’s a substitution of the main postulate with another that is easy to discredit. My intention in introducing the SE discussion was not to discredit Evolution, but to understand how Evolution can work when it APPEARS to violate some fundamental tenets of SE that are proven and widely accepted by rocket scientists like myself. My explanation of SE was correct, but it also implied a rigidity that clearly clashes with Evolution as you guys know it. It was never intended as a substitute to be used to discredit your beliefs. Rather it was introduced so you could understand my perspective and could help me navigate toward an understanding of Evolution that you have. You have done a good job in leading to that understanding. though you’re a bit grumpy and seem to take my inquiry as a personal attack on your beliefs. I’m not attacking anyone, and have not intention of doing so. I just want to understand your thinking. Seeing how the SE paradigm is interpreted within an evolutionary framework is helpful in guiding me to an understanding of your views. So in my view, it wasn’t and still isn’t a strawman.

Regarding my question about you “begging the question” when you claim that every time an animal has offspring, it proves me wrong, i.e., that the SE concept that requires coordinated change across all the components that contribute to that function. You’re assuming that you are correct (SE principals are not needed) to prove you are correct. You claim that every time an animal gives birth, it proves me wrong. Maybe I’m not smart enough to follow your logic, but it sounds like the fallacy, i.e., you’re right because you’re right.

Notwithstanding, I’m learning from you guys and it’s helping me better understand your thinking which is my goal. And I’m enjoying it. Most of all, I appreciate your patience. Who knows, you may in the end win me over to EC.


(Raymond Isbell) #47

Thanks. I’m drowning in things to read. I’m glad it snowed in DC. Shoveling snow gave my brain a break. It’s hurting right now.


(Raymond Isbell) #48

Thanks. Looks like just the kind of thing that I need to read.


(Raymond Isbell) #49

Regarding God’s sovereignty and freedom of nature including man’s, take a look at Molinism. Use of it with some modifications I’ve made, has helped to understand God’s sovereignty, man’s free will, and God’s ability to control history down to the minutest details. Makes perfect sense to me.


(James McKay) #50

I take it that by SE you mean software engineering?

Did you have any thoughts on my previous post about the subject? As I said, you’re looking at it through the lens of traditional software methodologies such as waterfall, change management, ITBM and so on, and I think that’s where you’re going wrong. Evolution, as these guys are describing it, has more in common with modern agile methodologies (continuous delivery, canary builds, phoenix servers, microservices, etc) than with traditional waterfall methodologies used by rocket scientists.


(Raymond Isbell) #51

Thanks Bill. SE often incorporates redundancy to reduce risk so yes, we can build all the “diversity” you’re seeing in the cell into any system we choose. The trade-off is cost, schedule, complexity (which make it difficult and costly to maintain), and performance. One of the things that I think you guys are overlooking in my challenges is that I state up-front that all the subsystems are interdependent. Think of today’s software which is often open for reuse. Accessing it is easy because the owner publishes an Application Programming Interface (API). This tells users of the software how to gain access and use the internal functionality of that software. If the owner changes his code (randomly or by design) and doesn’t update the API, users will find problems when they try to integrate that software into their software if they use the old API.


(Raymond Isbell) #52

No, SE - Systems Engineering


(Raymond Isbell) #53

The old traditional ways are not wrong, they’re just slow and unresponsive to new requirements. DevOps and AGILE are the new and more modern ways that have a faster turn-around for new requirements. Both are true. The old way was more formal, and led to tedium via the required bureaucracy with its V&V structure.


(Raymond Isbell) #54

I suspect that it’s far more complex that a single mutation. Bone length is not only genetic, but also probably epigenetic.


(Christy Hemphill) #55

Yes, that is where a lot of people end up.


(Steve Schaffner) #56

Suggestion: go back and read your own first post as if it weren’t written by you and see how you come across. Had you wanted to learn about evolution from those who know more about it, a good start would have been something like, “There’s a basic principle in SE that. . . How do biologists think evolution gets around this limitation?” Instead, your opening was more like this: “The entire field of evolutionary biology is ignorant of this basic principle that makes evolution impossible. Your thoughts?” This is not an approach that is likely to give a good impression – especially when the engineering principle in question is something that will have occurred to anyone with common sense who’s thought about the subject at any length.


(Steve Schaffner) #57

And here you’re doing it again. You asked a biologist a question, and in response you’re trying to correct his answer based on your gut feeling and admitted ignorance of the subject. Seriously, how would you respond to someone who didn’t know anything about the subject offering to correct you about basic SE?

To address the content. . . yes, your suspicion is incorrect. For example, single-nucleotide variants in an enhancer element controlling the gene GDF5 change expression of the gene and result in different bone length (Nat Genet. 2017 Aug;49(8):1202-1210).

You’re really not helping yourself here. This is roughly equivalent to saying, “Bone length is not only genetic, but also probably involves calcium chemistry.”


(Raymond Isbell) #58

My bad! I’ll try to be less confrontational (i.e., assuming I’m right and the EC folks are wrong.) Your way of phrasing the issue is much better. I’m learning on several fronts. Thanks.

Since you phrased it so nicely, what’s the answer? I know SE is true, but you guys are showing me that there’s more to the story. Showing how both are true appears to be my challenge. Building robustness, redundancy, etc. into a system can be done, but it’s more expensive, complicated, and difficult to change. It makes the probability #'s even less likely if it happens by chance.


(Steve Schaffner) #59

Great!

The broad answer is that a brittle system that cannot handle either genetic or environmental perturbation isn’t going to stick around very long and is therefore not the sort of organism that evolves. As to the probabilities – how are you calculating them?

Detailed mechanistic answers include lots of stuff – complex life doesn’t have one single solution. In the example I gave, of varying bone length, one important component is modularity, with weak coupling between modules. Bones, blood vessels, nerves, and muscles have largely independent development programs with only limited and flexible interactions between them. Blood vessels basically grow wherever they’re needed (in particular, wherever there isn’t much oxygen) without special instructions from the tissue, so it doesn’t matter how long a limb is. Nerves similarly grow until they find something useful to connect to; if they don’t, they kill themselves. Muscles end in tendons which attach themselves to molecular signals on patches of bone; as long as the signal is there, the precise length of the bone doesn’t matter. The signals on the bone are provided by yet another module separate from the formation of the bone itself, which makes them relatively easy to move around, evolutionarily speaking.


#60

Or to put this in terms @Raymond_Isbell will understand, biological systems are self modifying with little or no information exchange to coordinate the change. I would like to see a human built system do that.